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59 Repositories
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Repository
Owner
Contributors
Topics
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
Federico Marini
Single-cell sequencing
Python
RNA-seq
Transcriptomics
Days since last push
1390
License
-
https://www.sc-best-practices.org
Contributors
Lukas Heumos
Anna Schaar
Luke Zappia
Lisa Sikkema
seo
Single-cell sequencing
Transcriptomics
Python
Days since last push
0
License
other
Contributors
Meeta Mistry
marypiper
Radhika Khetani
Jihe Liu
Will Gammerdinger
Single-cell sequencing
Transcriptomics
RNA-seq
Days since last push
42
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
260
License
other
Contributors
Khushbu Patel
Transcriptomics
Single-cell sequencing
RNA-seq
Days since last push
730
License
mit
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
0
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
9
License
-
Contributors
Åsa Björklund
Roy Francis
Susanne Reinsbach
Jennifer Fransson
Marcel Martin
Single-cell sequencing
Transcriptomics
RNA-seq
Days since last push
157
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
1522
License
-
Contributors
Andy Coenen
Adam Pearce
Kyle Willett
Single-cell sequencing
Data visualization
Data science
Machine learning
Statistics
Days since last push
99
License
apache-2.0
Contributors
Vladimir (Vlad) Kiselev
tallulandrews
Cellular Genomics Informatics
Prete
Yihui Xie
Single-cell sequencing
RNA-seq
Transcriptomics
Days since last push
1515
License
gpl-3.0
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
53
License
mit
The rendered book can be found at https://liulab-dfci.github.io/bioinfo-combio/
mit
Contributors
Jack Kang
liulab-dfci
Gali Bai
Ming Tang
Maarten de Vries
General
Next generation sequencing
Transcriptomics
Genomics
ATAC-seq
ChIP-seq
Epigenetics
Single-cell sequencing
Variant analysis
Days since last push
1640
License
mit
110
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
147
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
259
License
cc-by-4.0
A course on genomics and bioinformatics from WashU
Contributors
Chris Miller
Jason Walker
John Garza
jennymckenzie
Kelsy Cotto
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
Code and data repository for the 2020 physalia course on single cell RNA sequencing.
Contributors
Kirk Gosik
Orr Ashenberg
Dana Silverbush
Single-cell sequencing
Transcriptomics
R
Days since last push
2360
License
-
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
2629
License
-
Trajectory inference and differential expression over multiple conditions in scRNA-seq
Contributors
Koen Van den Berge
Hector Roux de Bézieux
Single-cell sequencing
Transcriptomics
RNA-seq
Days since last push
1988
License
other
workshop website on readthedocs
Contributors
agata-sm
vincent-van-hoef
orzechoj
LouellaVasquez33
C. Navarro
Epigenetics
ChIP-seq
ATAC-seq
Single-cell sequencing
Next generation sequencing
Days since last push
122
License
-
SciLifeLab SIB Summer School for Advanced topics in Single Cell Omics. Site: https://nbisweden.github.io/single-cell_sib_scilifelab_2021/
Contributors
Emma Dann
Panagiotis Papasaikas
Åsa Björklund
greg-r-sib
Volker Bergen
Single-cell sequencing
Transcriptomics
RNA-seq
Days since last push
1838
License
-
Contributors
Gregor Sturm
Mikaela Koutrouli
Philipp A.
Isaac Virshup
Lukas Heumos
Single-cell sequencing
Transcriptomics
RNA-seq
Days since last push
3
License
bsd-3-clause
Based on their genomic data types and goals, this course will help learners find educational resources and tools to help them process and interpret data.
cc-by-4.0
Contributors
Candace Savonen
jhudsl-robot
cmills2
Carrie Wright
Kate Isaac
Genomics
Next generation sequencing
Transcriptomics
RNA-seq
Single-cell sequencing
Variant analysis
ATAC-seq
Spatial transcriptomics
Genome annotation
Epigenetics
ChIP-seq
Days since last push
1
License
cc-by-4.0
Material for lectures and exercises of the SIB course "Advanced topics in single-cell transcriptomics" (May 2020)
Contributors
Michael Stadler
Mike Smith
Avi Srivastava
Charlotte Soneson
Single-cell sequencing
Transcriptomics
RNA-seq
Days since last push
2316
License
-
Topics