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100 Repositories
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Repository
Owner
Contributors
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Stargazers
Days since last push
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
Contributors
MalteDLuecken
Lukas Heumos
Leander
lzhus
Philipp A.
Single-cell sequencing
Python
RNA-seq
Transcriptomics
Days since last push
1423
License
-
Contributors
Meeta Mistry
marypiper
Radhika Khetani
Will Gammerdinger
Jihe Liu
Single-cell sequencing
Transcriptomics
RNA-seq
Days since last push
75
License
-
Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023
Contributors
tarachari3
Meichen Fang
Lior Pachter
Zitong Jerry Wang
Laura Luebbert, Ph.D.
General
Statistics
Next generation sequencing
Genomics
Single-cell sequencing
Transcriptomics
RNA-seq
Days since last push
294
License
other
Contributors
Khushbu Patel
Transcriptomics
Single-cell sequencing
RNA-seq
Days since last push
763
License
mit
Materials for short, half-day workshops
Contributors
marypiper
Will Gammerdinger
Radhika Khetani
Meeta Mistry
eberdan
General
Python
R
Rmarkdown
Unix/Linux
Version control
Enrichment analysis
FAIR data
Data visualization
Variant analysis
RNA-seq
Transcriptomics
Days since last push
104
License
other
Contributors
Helena
Saskia Hiltemann
Bérénice Batut
Björn Grüning
Wendi Bacon
Galaxy
General
Genomics
Next generation sequencing
Transcriptomics
RNA-seq
Single-cell sequencing
Variant analysis
ATAC-seq
Comparative genomics
ChIP-seq
Epigenetics
Genome annotation
Genome assembly
Metagenomics
Microbiology
Long read sequencing
Metabolomics
Proteomics
Data management
FAIR data
Reproducibility
Data science
Statistics
Machine learning
Snakemake
R
Python
Unix/Linux
Version control
Days since last push
1
License
mit
Workshops presented by the Gladstone Bioinformatics Core
Contributors
Natalie Gill
Ayushi Agrawal
reubenthomas
Kristina Hanspers
MichelaTr
General
R
Version control
Genomics
Transcriptomics
Single-cell sequencing
RNA-seq
Pathways and Networks
Data visualization
Statistics
ATAC-seq
Machine learning
Unix/Linux
Days since last push
28
License
-
Contributors
Åsa Björklund
Roy Francis
Susanne Reinsbach
Jennifer Fransson
Marcel Martin
Single-cell sequencing
Transcriptomics
RNA-seq
Days since last push
0
License
cc-by-4.0
Single RNA-seq data analysis with R (Finland, May, 2019)
Contributors
OLRAEN
Eija Korpelainen
Åsa Björklund
Rui Benfeitas
ahmedmahfouz
Single-cell sequencing
Transcriptomics
RNA-seq
Days since last push
1556
License
-
Contributors
Meeta Mistry
Radhika Khetani
marypiper
Will Gammerdinger
Jihe Liu
Transcriptomics
RNA-seq
Days since last push
159
License
-
Contributors
Rick Masonbrink
Arun Seetharam
Andrew Severin
Siva Chudalayandi
Aleksandra E. Badaczewska-Dawid
General
Nextflow
Workflows
Data management
Data visualization
Unix/Linux
ATAC-seq
Comparative genomics
Epigenetics
Genome annotation
Genome assembly
Metagenomics
RNA-seq
Transcriptomics
Variant analysis
Days since last push
96
License
mit
Contributors
Vladimir (Vlad) Kiselev
tallulandrews
Cellular Genomics Informatics
Prete
Yihui Xie
Single-cell sequencing
RNA-seq
Transcriptomics
Days since last push
1549
License
gpl-3.0
Introduction to bulk RNA-seq
Contributors
Radhika Khetani
Meeta Mistry
Will Gammerdinger
Jihe Liu
eberdan
Transcriptomics
RNA-seq
Days since last push
232
License
-
Contributors
Malachi Griffith
Kelsy Cotto
Obi Griffith
Huiming Xia
Kartik Singhal
RNA-seq
Unix/Linux
R
Next generation sequencing
Single-cell sequencing
Days since last push
3
License
mit
Melbourne Bioinformatics documentation in markdown format
Contributors
Vini Salazar
Vicky Perreau
Clare Sloggett
Simon Gladman
Anna Syme
General
Unix/Linux
Data management
Transcriptomics
RNA-seq
Genomics
Version control
Days since last push
92
License
-
111
The package wrapping the book, for deployment via the Bioconductor build system.
Contributors
actions-user
Aaron Lun
Hervé Pagès
Alan O'Callaghan
Nitesh Turaga
Single-cell sequencing
Transcriptomics
RNA-seq
Next generation sequencing
R
Days since last push
180
License
-
SIB course on single cell transcriptomics by mostly using the Seurat pipeline
cc-by-4.0
Contributors
Geert van Geest
TaniaW
Rachel Marcone
Single-cell sequencing
Transcriptomics
RNA-seq
Days since last push
292
License
cc-by-4.0
A course on genomics and bioinformatics from WashU
Contributors
Chris Miller
Jason Walker
John Garza
jennymckenzie
Susanna Kiwala
Genomics
Next generation sequencing
RNA-seq
Variant analysis
Data visualization
Long read sequencing
Single-cell sequencing
Days since last push
0
License
-
A collection of modules that are combined into 1-5 day workshops on computational topics for the childhood cancer research community.
Contributors
Joshua Shapiro
Stephanie J. Spielman
Jaclyn Taroni
Ally Hawkins
Candace Savonen
General
Transcriptomics
RNA-seq
Single-cell sequencing
R
Pathways and Networks
Days since last push
1
License
other
This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
gpl-3.0
Contributors
Aurelien Dugourd
Javier Perales-Paton
Attila Gabor
Olga Ivanova
Charlotte Boys
Transcriptomics
RNA-seq
Next generation sequencing
Days since last push
1300
License
gpl-3.0
Tutorials and code for ISMB 2019 short course on Recent Advances in Statistical Methods and Computational Algorithms for Single-Cell Omics Analysis
Contributors
Yuchao Jiang
Rhonda Bacher
Jingshu Wang
Single-cell sequencing
RNA-seq
Transcriptomics
Days since last push
2663
License
-
Contributors
Roy Francis
Nima Rafati
jlorent
Jeanette Tångrot
Johan
Transcriptomics
RNA-seq
Next generation sequencing
Days since last push
964
License
gpl-3.0
This RNAseq data analysis tutorial is created for educational purpose
Contributors
Amarinder Singh Thind
Transcriptomics
RNA-seq
Next generation sequencing
Days since last push
259
License
-
course about NGS data processing: genomics and transcriptomics
gpl-3.0
Contributors
Boas Pucker
Next generation sequencing
Transcriptomics
RNA-seq
Genomics
Days since last push
263
License
gpl-3.0
Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor
Contributors
Charlotte Soneson
Jenny Drnevich
Zhian N. Kamvar
Zuguang Gu
Givanna Putri
Transcriptomics
RNA-seq
R
Days since last push
1
License
other
Topics