Genomic Data Science Specialization

About Course

Genomic Data Science Specialization, With genomics sparks a revolution in medical discoveries, it becomes imperative to be able to better understand the genome, and be able to leverage the data and information from genomic datasets. Genomic Data Science is the field that applies statistics and data science to the genome. This Specialization covers the concepts and tools to understand, analyze, and interpret data from next generation sequencing experiments. It teaches the most common tools used in genomic data science including how to use the command line, along with a variety of software implementation tools like Python, R, and Bioconductor. This Specialization is designed to serve as both a standalone introduction to genomic data science or as a perfect compliment to a primary degree or postdoc in biology, molecular biology, or genetics, for scientists in these fields seeking to gain familiarity in data science and statistical tools to better interact with the data in their everyday work.

Course Content

01. Introduction to Genomic Technologies

001 01_syllabus_instructions.html

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003 02_pre-course-survey_instructions.html

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007 03_why-genomics.mp4

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011 04_what-is-genomics.mp4

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015 05_what-is-genomic-data-science.mp4

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019 01_just-enough-cell-biology.mp4

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023 02_important-molecules-in-molecular-biology.mp4

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027 03_the-human-genome-project.mp4

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031 04_molecular-biology-structures.mp4

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035 05_from-genes-to-phenotypes.mp4

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040 01_polymerase-chain-reaction.mp4

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044 02_next-generation-sequencing.mp4

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048 03_applications-of-sequencing.mp4

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053 01_what-is-computer-science.mp4

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057 02_algorithms.mp4

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061 03_memory-and-data-structures.mp4

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065 04_efficiency.mp4

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069 05_software-engineering.mp4

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073 06_what-is-computational-biology-software.mp4

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078 01_why-care-about-statistics.mp4

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082 02_what-went-wrong.mp4

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086 03_the-central-dogma-of-statistics.mp4

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090 04_data-sharing-plans.mp4

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094 05_getting-help-with-statistics.mp4

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098 06_plotting-your-data.mp4

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102 07_sample-size-and-variability.mp4

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106 08_statistical-significance.mp4

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110 09_multiple-testing.mp4

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114 10_study-design-batch-effects-and-confounding.mp4

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115 01_quiz-4-data-science-technology_exam.html

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119 02_course-project_exam.html

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120 01_post-course-survey_instructions.html

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links.txt

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02. Python for Genomic Data Science

001 01_welcome_instructions.html

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002 02_pre-course-survey_instructions.html

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003 03_syllabus_instructions.html

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008 04_lecture-1-overview-of-python.mp4

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009 05_lecture-1-quiz_exam.html

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013 06_lecture-2-1-first-steps-toward-programming-part-1.mp4

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016 07_lecture-2-2-first-steps-toward-programming-part-2.mp4

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019 08_lecture-2-3-first-steps-toward-programming-part-3-8-57.mp4

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022 09_lecture-2-4-first-steps-toward-programming-part-4-9-58.mp4

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023 10_lecture-2-quiz_exam.html

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027 01_lecture-3-1-data-structures-part-1-11-58.mp4

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030 02_lecture-3-2-data-structures-part-2-10-41.mp4

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031 03_lecture-3-quiz_exam.html

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035 04_lecture-4-1-ifs-and-loops-part-1-11-26.mp4

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038 05_lecture-4-2-ifs-and-loops-part-2-15-28.mp4

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039 06_lecture-4-quiz_exam.html

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043 01_lecture-5-1-functions-part-1-5-54.mp4

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046 02_lecture-5-2-functions-part-2-8-20.mp4

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049 03_lecture-5-3-functions-part-3-13-24.mp4

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050 04_lecture-5-quiz_exam.html

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054 05_lecture-6-modules-and-packages-10-32.mp4

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055 06_lecture-6-quiz_exam.html

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059 01_lecture-7-1-communicating-with-the-outside-part-1-6-41.mp4

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062 02_lecture-7-2-communicating-with-the-outside-part-2-7-38.mp4

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065 03_lecture-7-3-communicating-with-the-outside-part-3-17-42.mp4

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066 04_lecture-7-quiz_exam.html

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070 05_lecture-8-biopython-13-32.mp4

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071 06_lecture-8-quiz_exam.html

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073 01_final-exam-instructions_instructions.html

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074 02_final-exam-read-instructions-first_exam.html

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075 01_post-course-survey_instructions.html

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03. Algorithms for DNA Sequencing

002 02_pre-course-survey_instructions.html

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003 03_syllabus_instructions.html

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008 04_setting-up-python-and-jupyter_install.html

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010 05_getting-slides-and-notebooks_instructions.html

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011 06_using-data-files-with-python-programs_instructions.html

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014 01_module-1-introduction.mp4

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020 02_lecture-why-study-this.mp4

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024 03_lecture-dna-sequencing-past-and-present.mp4

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030 04_lecture-genomes-as-strings-reads-as-substrings.mp4

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034 05_lecture-string-definitions-and-python-examples.mp4

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037 06_practical-string-basics.mp4

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042 07_practical-manipulating-dna-strings.mp4

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045 08_practical-downloading-and-parsing-a-genome.mp4

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049 09_lecture-how-dna-gets-copied.mp4

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052 10_optional-lecture-how-second-generation-sequencers-work.mp4

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055 11_optional-lecture-sequencing-errors-and-base-qualities.mp4

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059 12_lecture-sequencing-reads-in-fastq-format.mp4

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062 13_practical-working-with-sequencing-reads.mp4

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065 14_practical-analyzing-reads-by-position.mp4

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069 15_lecture-sequencers-give-pieces-to-genomic-puzzles.mp4

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073 16_lecture-read-alignment-and-why-its-hard.mp4

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077 17_lecture-naive-exact-matching.mp4

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001 01_welcome-to-algorithms-for-dna-sequencing_instructions.html

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080 18_practical-matching-artificial-reads.mp4

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083 19_practical-matching-real-reads.mp4

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084 01_module-1_exam.html

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088 02_programming-homework-1_exam.html

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091 01_week-2-introduction.mp4

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095 02_lecture-boyer-moore-basics.mp4

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099 03_lecture-boyer-moore-putting-it-all-together.mp4

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103 04_lecture-diversion-repetitive-elements.mp4

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106 05_practical-implementing-boyer-moore.mp4

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110 06_lecture-preprocessing.mp4

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114 07_lecture-indexing-and-the-k-mer-index.mp4

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118 08_lecture-ordered-structures-for-indexing.mp4

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122 09_lecture-hash-tables-for-indexing.mp4

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125 10_practical-implementing-a-k-mer-index.mp4

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129 11_lecture-variations-on-k-mer-indexes.mp4

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133 12_lecture-genome-indexes-used-in-research.mp4

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137 13_lecture-approximate-matching-hamming-and-edit-distance.mp4

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141 14_lecture-pigeonhole-principle.mp4

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144 15_practical-implementing-the-pigeonhole-principle.mp4

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145 01_module-2_exam.html

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151 02_programming-homework-2_exam.html

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154 01_module-3-introduction.mp4

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158 02_lecture-solving-the-edit-distance-problem.mp4

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161 03_lecture-using-dynamic-programming-for-edit-distance.mp4

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164 04_practical-implementing-dynamic-programming-for-edit-distance.mp4

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168 05_lecture-a-new-solution-to-approximate-matching.mp4

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172 06_lecture-meet-the-family-global-and-local-alignment.mp4

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175 07_practical-implementing-global-alignment.mp4

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179 08_lecture-read-alignment-in-the-field.mp4

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183 09_lecture-assembly-working-from-scratch.mp4

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187 10_lecture-first-and-second-laws-of-assembly.mp4

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191 11_lecture-overlap-graphs.mp4

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194 12_practical-overlaps-between-pairs-of-reads.mp4

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197 13_practical-finding-and-representing-all-overlaps.mp4

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198 01_module-3_exam.html

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201 02_programming-homework-3_exam.html

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204 01_module-4-introduction.mp4

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208 02_lecture-the-shortest-common-superstring-problem.mp4

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211 03_practical-implementing-shortest-common-superstring.mp4

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215 04_lecture-greedy-shortest-common-superstring.mp4

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218 05_practical-implementing-greedy-shortest-common-superstring.mp4

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222 06_lecture-third-law-of-assembly-repeats-are-bad.mp4

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226 07_lecture-de-bruijn-graphs-and-eulerian-walks.mp4

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229 08_practical-building-a-de-bruijn-graph.mp4

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233 09_lecture-when-eulerian-walks-go-wrong.mp4

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237 10_lecture-assemblers-in-practice.mp4

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241 11_lecture-the-future-is-long.mp4

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245 12_lecture-computer-science-and-life-science.mp4

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248 13_lecture-thank-yous.mp4

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249 01_programming-homework-4_exam.html

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04. Command Line Tools for Genomic Data Science

002 02_syllabus_instructions.html

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008 03_vmbox-download-instructions_instructions.html

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011 04_docker-image-download-instructions_instructions.html

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012 05_pre-course-survey_instructions.html

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016 01_basic-unix-commands-1-content-representation.mp4

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020 02_basic-unix-commands-2-files-directories-paths.mp4

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024 03_basic-unix-commands-3-file-naming.mp4

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028 04_basic-unix-commands-4-content-creation.mp4

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032 05_basic-unix-commands-5-accessing-content-i.mp4

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036 06_basic-unix-commands-6-accessing-content-ii.mp4

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040 07_basic-unix-commands-7-redirecting-content.mp4

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044 08_basic-unix-commands-8-querying-content.mp4

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048 09_basic-unix-commands-9-comparing-content.mp4

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052 10_basic-unix-commands-10-archiving-content.mp4

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056 11_basic-unix-commands-11-practical-exercises-i.mp4

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060 12_basic-unix-commands-12-practical-exercises-ii.mp4

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061 01_module-1-quiz_exam.html

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063 02_module-1-exam-instructions-important_instructions.html

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064 03_module-1-exam_exam.html

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068 01_sequences-and-genomic-features-1-molecular-bio-primer.mp4

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072 02_sequences-and-genomic-features-2-sequence-representation-and-generation.mp4

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076 03_sequences-and-genomic-features-3-annotation.mp4

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080 04_sequences-and-genomic-features-4-1-alignment-i.mp4

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084 05_sequences-and-genomic-features-4-2-alignment-ii.mp4

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088 06_sequences-and-genomic-features-5-recreating-sequences-features.mp4

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092 07_sequences-and-genomic-features-6-genomic-feature-retrieval.mp4

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096 08_sequences-and-genomic-features-7-samtools-i.mp4

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100 09_sequences-and-genomic-features-8-samtools-ii.mp4

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104 10_sequences-and-genomic-features-9-bedtools-i.mp4

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108 11_sequences-and-genomic-features-10-bedtools-ii.mp4

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109 01_module-2-quiz_exam.html

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111 02_module-2-exam-instructions-important_instructions.html

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112 03_module-2-exam_exam.html

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116 01_alignment-sequence-variation-1-overview.mp4

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120 02_alignment-sequence-variation-2-alignment-variant-detection-tools.mp4

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124 03_alignment-sequence-variation-3-vcf.mp4

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128 04_alignment-sequence-variation-4-bowtie.mp4

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131 05_alignment-sequence-variation-5-bwa.mp4

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135 06_alignment-sequence-variation-6-samtools-mpileup.mp4

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139 07_alignment-sequence-variation-7-bcftools.mp4

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143 08_alignment-sequence-variation-8-variant-calling.mp4

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144 01_module-3-quiz_exam.html

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146 02_module-3-exam-instructions-important_instructions.html

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147 03_module-3-exam_exam.html

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151 01_tools-for-transcriptomics-1-overview.mp4

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155 02_tools-for-transcriptomics-2-rna-seq.mp4

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159 03_tools-for-transcriptomics-3-1-tophat-i.mp4

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162 04_tools-for-transcriptomics-3-2-tophat-ii.mp4

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166 05_tools-for-transcriptomics-4-cufflinks.mp4

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170 06_tools-for-transcriptomics-5-cuffdiff.mp4

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174 07_tools-for-transcriptomics-6-1-integrated-genomics-viewer-i.mp4

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177 08_tools-for-transcriptomics-6-2-integrated-genomics-viewer-ii.mp4

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178 01_module-4-quiz_exam.html

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180 02_module-4-exam-instructions-important_instructions.html

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181 03_module-4-exam_exam.html

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182 01_post-course-survey_instructions.html

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05. Bioconductor for Genomic Data Science

002 02_syllabus_instructions.html

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004 03_pre-course-survey_instructions.html

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007 01_installing-r-on-windows.mp4

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010 02_installing-r-on-a-mac.mp4

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013 03_installing-r-studio-on-a-mac.mp4

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017 01_what-is-bioconductor.mp4

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021 02_installing-bioconductor.mp4

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025 03_the-bioconductor-website.mp4

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029 04_useful-online-resources.mp4

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033 05_r-base-types.mp4

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037 06_granges-overview.mp4

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041 07_iranges-basic-usage.mp4

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045 08_genomicranges-granges.mp4

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049 09_genomicranges-basic-granges-usage.mp4

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053 10_genomicranges-seqinfo.mp4

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057 11_annotationhub.mp4

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061 12_usecase-annotationhub-and-granges-part-1.mp4

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065 13_usecase-annotationhub-and-granges-part-2.mp4

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070 01_biostrings.mp4

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074 02_bsgenome.mp4

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078 03_biostrings-matching.mp4

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082 04_bsgenome-views.mp4

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086 05_genomicranges-rle.mp4

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090 06_genomicranges-lists.mp4

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094 07_genomicfeatures.mp4

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098 08_rtracklayer-data-import.mp4

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103 01_basic-data-types.mp4

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107 02_annotation-overview.mp4

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111 03_expressionset-overview.mp4

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115 04_expressionset.mp4

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119 05_summarizedexperiment.mp4

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123 06_geoquery.mp4

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127 07_biomart.mp4

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131 08_r-s4-classes.mp4

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135 09_r-s4-methods.mp4

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140 01_getting-data-into-bioconductor.mp4

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144 02_short-read.mp4

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148 03_rsamtools.mp4

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152 04_oligo.mp4

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156 05_limma.mp4

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160 06_minfi.mp4

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164 07_count-based-rna-seq-analysis.mp4

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165 01_quiz-4_exam.html

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06. Statistics for Genomic Data Science

004 02_syllabus_instructions.html

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006 03_pre-course-survey_instructions.html

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007 04_introduction-and-materials_instructions.html

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010 05_what-is-statistics.mp4

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013 06_finding-statistics-you-can-trust-4-44.mp4

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016 07_getting-help-3-44.mp4

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019 08_what-is-data-4-28.mp4

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022 09_representing-data-5-23.mp4

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025 01_module-1-overview-1-07.mp4

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028 02_reproducible-research-3-42.mp4

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031 03_achieving-reproducible-research-5-02.mp4

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035 04_r-markdown-6-26.mp4

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038 05_the-three-tables-in-genomics-2-10.mp4

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042 06_the-three-tables-in-genomics-in-r-3-46.mp4

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045 07_experimental-design-variability-replication-and-power-14-17.mp4

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048 08_experimental-design-confounding-and-randomization-9-26.mp4

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052 09_exploratory-analysis-9-21.mp4

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056 10_exploratory-analysis-in-r-part-i-7-22.mp4

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060 11_exploratory-analysis-in-r-part-ii-10-07.mp4

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063 12_exploratory-analysis-in-r-part-iii-7-26.mp4

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067 13_data-transforms-7-31.mp4

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071 14_clustering-8-43.mp4

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075 15_clustering-in-r-9-09.mp4

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079 01_module-2-overview-1-12.mp4

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082 02_dimension-reduction-12-13.mp4

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086 03_dimension-reduction-in-r-8-48.mp4

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089 04_pre-processing-and-normalization-11-26.mp4

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093 05_quantile-normalization-in-r-4-49.mp4

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096 06_the-linear-model-6-50.mp4

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099 07_linear-models-with-categorical-covariates-4-08.mp4

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102 08_adjusting-for-covariates-4-16.mp4

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106 09_linear-regression-in-r-13-03.mp4

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109 10_many-regressions-at-once-3-50.mp4

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113 11_many-regressions-in-r-7-21.mp4

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116 12_batch-effects-and-confounders-7-11.mp4

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120 13_batch-effects-in-r-part-a-8-18.mp4

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123 14_batch-effects-in-r-part-b-3-50.mp4

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127 01_module-3-overview-1-07.mp4

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130 02_logistic-regression-7-03.mp4

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133 03_regression-for-counts-5-02.mp4

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137 04_glms-in-r-9-28.mp4

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140 05_inference-4-18.mp4

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143 06_null-and-alternative-hypotheses-4-45.mp4

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146 07_calculating-statistics-5-11.mp4

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149 08_comparing-models-7-08.mp4

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153 09_calculating-statistics-in-r.mp4

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156 10_permutation-3-26.mp4

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160 11_permutation-in-r-3-33.mp4

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163 12_p-values-6-04.mp4

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166 13_multiple-testing-8-25.mp4

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003 01_welcome-to-statistics-for-genomic-data-science.mp4

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170 14_p-values-and-multiple-testing-in-r-part-a-5-58.mp4

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173 15_p-values-and-multiple-testing-in-r-part-b-4-23.mp4

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177 01_module-4-overview-1-21.mp4

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180 02_gene-set-enrichment-4-19.mp4

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183 03_more-enrichment-3-59.mp4

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187 04_gene-set-analysis-in-r-7-43.mp4

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190 05_the-process-for-rna-seq-3-59.mp4

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193 06_the-process-for-chip-seq-5-25.mp4

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196 07_the-process-for-dna-methylation-5-03.mp4

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199 08_the-process-for-gwas-wgs-6-12.mp4

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202 09_combining-data-types-eqtl-6-04.mp4

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206 10_eqtl-in-r-10-36.mp4

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209 11_researcher-degrees-of-freedom-5-49.mp4

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212 12_inference-vs-prediction-8-52.mp4

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215 13_knowing-when-to-get-help-2-31.mp4

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218 14_statistics-for-genomic-data-science-wrap-up-1-53.mp4

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219 01_module-4-quiz_exam.html

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links.txt

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About Course

What Will You Learn?

Course Content

01. Introduction to Genomic Technologies

001 01_syllabus_instructions.html

003 02_pre-course-survey_instructions.html

007 03_why-genomics.mp4

011 04_what-is-genomics.mp4

015 05_what-is-genomic-data-science.mp4

019 01_just-enough-cell-biology.mp4

023 02_important-molecules-in-molecular-biology.mp4

027 03_the-human-genome-project.mp4

031 04_molecular-biology-structures.mp4

035 05_from-genes-to-phenotypes.mp4

040 01_polymerase-chain-reaction.mp4

044 02_next-generation-sequencing.mp4

048 03_applications-of-sequencing.mp4

053 01_what-is-computer-science.mp4

057 02_algorithms.mp4

061 03_memory-and-data-structures.mp4

065 04_efficiency.mp4

069 05_software-engineering.mp4

073 06_what-is-computational-biology-software.mp4

078 01_why-care-about-statistics.mp4

082 02_what-went-wrong.mp4

086 03_the-central-dogma-of-statistics.mp4

090 04_data-sharing-plans.mp4

094 05_getting-help-with-statistics.mp4

098 06_plotting-your-data.mp4

102 07_sample-size-and-variability.mp4

106 08_statistical-significance.mp4

110 09_multiple-testing.mp4

114 10_study-design-batch-effects-and-confounding.mp4

115 01_quiz-4-data-science-technology_exam.html

119 02_course-project_exam.html

120 01_post-course-survey_instructions.html

links.txt

02. Python for Genomic Data Science

001 01_welcome_instructions.html

002 02_pre-course-survey_instructions.html

003 03_syllabus_instructions.html

008 04_lecture-1-overview-of-python.mp4

009 05_lecture-1-quiz_exam.html

013 06_lecture-2-1-first-steps-toward-programming-part-1.mp4

016 07_lecture-2-2-first-steps-toward-programming-part-2.mp4

019 08_lecture-2-3-first-steps-toward-programming-part-3-8-57.mp4

022 09_lecture-2-4-first-steps-toward-programming-part-4-9-58.mp4

023 10_lecture-2-quiz_exam.html

027 01_lecture-3-1-data-structures-part-1-11-58.mp4

030 02_lecture-3-2-data-structures-part-2-10-41.mp4

031 03_lecture-3-quiz_exam.html

035 04_lecture-4-1-ifs-and-loops-part-1-11-26.mp4

038 05_lecture-4-2-ifs-and-loops-part-2-15-28.mp4

039 06_lecture-4-quiz_exam.html

043 01_lecture-5-1-functions-part-1-5-54.mp4

046 02_lecture-5-2-functions-part-2-8-20.mp4

049 03_lecture-5-3-functions-part-3-13-24.mp4

050 04_lecture-5-quiz_exam.html

054 05_lecture-6-modules-and-packages-10-32.mp4

055 06_lecture-6-quiz_exam.html

059 01_lecture-7-1-communicating-with-the-outside-part-1-6-41.mp4

062 02_lecture-7-2-communicating-with-the-outside-part-2-7-38.mp4

065 03_lecture-7-3-communicating-with-the-outside-part-3-17-42.mp4

066 04_lecture-7-quiz_exam.html

070 05_lecture-8-biopython-13-32.mp4

071 06_lecture-8-quiz_exam.html

073 01_final-exam-instructions_instructions.html

074 02_final-exam-read-instructions-first_exam.html

075 01_post-course-survey_instructions.html

03. Algorithms for DNA Sequencing

002 02_pre-course-survey_instructions.html

003 03_syllabus_instructions.html

008 04_setting-up-python-and-jupyter_install.html

010 05_getting-slides-and-notebooks_instructions.html

011 06_using-data-files-with-python-programs_instructions.html

014 01_module-1-introduction.mp4

020 02_lecture-why-study-this.mp4

024 03_lecture-dna-sequencing-past-and-present.mp4

030 04_lecture-genomes-as-strings-reads-as-substrings.mp4

034 05_lecture-string-definitions-and-python-examples.mp4