Course Content
In-Depth Introduction to RNA-Seq
0/2
In-depth Introduction to RNA-Seq Data Analysis
44:08
Introduction to ArrayExpress
09:56
Genomic Databases for Raw Data
0/17
BioProject
06:40
BioSystems
04:16
BioSample
02:56
Introduction to Gene Expression Omnibus Database
09:16
Gene Expression Omnibus – Platforms
05:42
Gene Expression Omnibus – Samples
04:16
Gene Expression Omnibus – Series
04:01
Gene Expression Omnibus – Datasets
04:45
Gene Expression Omnibus – Profiles – How to Search for Gene Expression Profiles
05:55
NCBI Genomes & NCBI Assembly
36:14
Genome Reference Consortium
07:48
Introducton to Phytozome
09:39
Download an Entire Plant Genome & Proteome
26:41
Introduction to UCSC Genome Browser
13:40
How to retrieve an entire genome & Retrieval of SARS-CoV-2 Viral Genome
09:41
Introduction to ENSEMBL
07:50
Genome Assembly Retrieval and Analysis
10:24
File Formats
0/4
BED
04:27
GTF/GFF
11:07
SAM
09:07
FASTQ
18:02
RNA-Seq Data Analysis Pipeline (Theoretical & Practical)
0/18
Introduction to Anaconda for Bioinformatics and NGS
22:46
Introduction to Jupyter-Notebook for NGS Analysis
17:14
How to Retreive Raw Reads for RNA-Seq Data Analysis
03:26
Retrieval of Data Required for this Course
08:45
Setting Up Python Environment for RNA-Seq Analysis
00:00
In-depth Theory: Quality Control
19:37
Practical: Preprocess Raw Reads Using FASTQC, FASTP, Trimmomatic & Cutadapt
00:00
In-depth Theory: Mapping & Transcriptome Assembly
48:22
Practical: Mapping Preprocessed Reads Against a Reference Genome Using HISAT2, TOPHAT2, BOWTIE2, STAR
31:51
Practical: Transcriptome Assembly Using StringTie
00:00
Mapping Visualization & Evaluation
36:37
In-depth Theory: Gene Quantification, Expression Estimation & Differential Gene Expression
18:28
In-depth Theory: DeSeq2, Ballgown, edgeR
32:22
Differential Expression Analysis With PyDESeq2
00:00
Theory: Functinal Enrichment Analysis of the DEGs
18:39
Practial: Gene Ontology Analysis
28:02
Practical: Pathways Analysis Using KEGG, PANTHER, Reactome
12:41
Practical: Protein-Protein Interaction Using STRING
00:00
End-to-End RNA-Seq Data Analysis With Python-Based Pipeline
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