Course: Bioinformatics Methods for Transcriptomics
Modules:
Course Introduction, Gene expression analysis of RNA-seq data, Step 1: Downloading and Preparing the Data, Step 2: Aligning the RNA-seq reads, Step 3: Assembling the Genes and Transcripts, Part 1, Step 3: Assembling the Genes and Transcripts, Part 2, Step 4: Determining the Differentially Expressed Genes, Part 1, Step 4: Determining the Differentially Expressed Genes, Part 2, Step 4: Determining the Differentially Expressed Genes, Part 3, Step 4: Determining the Differentially Expressed Genes, Part 4, Step 4: Determining the Differentially Expressed Genes, Part 5, Step 5: Visualizing the Data, Part 1, Step 5: Visualizing the Data, Part 2
Introduction to alternative splicing (AS) analysis, Part 1, Introduction to alternative splicing (AS) analysis, Part 2, Introduction to alternative splicing (AS) analysis, Part 3, Step 1: Preparing the input data, Step 2: Isoform-level analysis with Cuffdiff2, Step 3: Event-level analysis with rMATS, Part 1, Step 3: Event-level analysis with rMATS, Part 2, Step 3: Event-level analysis with rMATS, Part 3, Step 4A: Intron-level analysis with MntJULiP, Part 1, Step 4A: Intron-level analysis with MntJULiP, Part 2, Step 4A: Intron-level analysis with MntJULiP, Part 3, Step 4A: Intron-level analysis with MntJULiP, Part 4, Step 4B: Intron-level analysis with MntJULiP II, Step 5A: Intron retention analysis with IRFinder, Part 1, Step 5A: Intron retention analysis with IRFinder, Part 2, Step 5A: Intron retention analysis with IRFinder, Part 3, Step 5B: Intron retention analysis with IRFinder II, Part 1, Step 5B: Intron retention analysis with IRFinder II, Part 2, Step 6A: AS visualization with IGV and Jutils I, Part 1, Step 6A: AS visualization with IGV and Jutils I, Part 2, Step 6B: AS visualization with Jutils II, Part 1, Step 6B: AS visualization with Jutils II, Part 2, Step 6B: AS visualization with Jutils II, Part 3, Step 6B: AS visualization with Jutils II, Part 4
Introduction to transcriptomics with long RNA sequencing reads, Preparing the input sequence data, Aligning the long RNA sequencing reads, Part 1, Aligning the long RNA sequencing reads, Part 2, Building transcript models with FLAIR (align), Building transcript models with FLAIR, Building transcript models with FLAIR (collapse), Part 1, Building transcript models with FLAIR (collapse), Part 2, Building transcript models with FLAIR (quantify), Building transcript models with IsoQuant, Part 1, Building transcript models with IsoQuant, Part 2, Building transcript models with IsoQuant, Part 3, Visualizing transcript data with the IGV, Part 1, Visualizing transcript data with the IGV, Part 2
Introduction to differential expression and splicing analysis with long read RNA sequencing, Preparing the data - a review, Differential gene and transcript expression (DESeq2), Part 1, Differential gene and transcript expression (DESeq2), Part 2, Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 1, Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 2, Differential splicing detection with short read tools (FLAIR diffSplice), Part 1, Differential splicing detection with short read tools (FLAIR diffSplice), Part 2, Differential splicing detection with short read tools (FLAIR diffSplice), Part 3, Differential splicing detection with long read tools (1) (LIQA), Part 1, Differential splicing detection with long read tools (1) (LIQA), Part 2, Differential splicing detection with long read tools (2) (LIQA), Part 1, Differential splicing detection with long read tools (2) (LIQA), Part 2, Differential splicing detection with long read tools (2) (LIQA), Part 3, Closing