95 results found Sort:

RNAseq analysis notes from Ming Tang
Created 2015-08-26
322 commits to master branch, last one 3 years ago
713
942
mit
157
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Created 2018-03-29
5,806 commits to master branch, last one 4 days ago
https://www.sc-best-practices.org
Created 2021-08-13
643 commits to master branch, last one about a month ago
164
780
gpl-3.0
38
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Created 2015-03-19
1,907 commits to master branch, last one 9 months ago
212
691
other
43
Tools to process and analyze deep sequencing data.
Created 2013-07-08
3,487 commits to master branch, last one 9 months ago
173
665
bsd-2-clause
48
Near-optimal RNA-Seq quantification
Created 2014-11-13
1,401 commits to master branch, last one 3 months ago
69
606
mit
11
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Created 2022-11-22
331 commits to main branch, last one 7 days ago
119
501
unknown
14
NicheNet: predict active ligand-target links between interacting cells
Created 2018-02-05
495 commits to master branch, last one 3 months ago
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
Created 2016-06-25
269 commits to master branch, last one 6 days ago
Customizable workflows based on snakemake and python for the analysis of NGS data
Created 2016-03-23
4,059 commits to master branch, last one 2 months ago
79
338
other
31
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
Created 2015-03-30
3,995 commits to develop branch, last one 7 days ago
Table of software for the analysis of single-cell RNA-seq data.
Created 2016-09-09
3,643 commits to main branch, last one about a month ago
95
305
gpl-3.0
39
Differential analysis of RNA-Seq
Created 2015-02-13
661 commits to master branch, last one 2 years ago
This repository has no description...
Created 2021-11-29
119 commits to main branch, last one 2 months ago
68
275
gpl-3.0
13
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
Created 2017-06-20
291 commits to main branch, last one about a year ago
minimal example implementations for bioinformatics workflow managers
Created 2020-09-14
142 commits to master branch, last one 3 years ago
50
229
other
14
Fast and accurate gene fusion detection from RNA-Seq data
Created 2017-10-23
694 commits to master branch, last one about a year ago
38
220
gpl-3.0
5
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
Created 2019-08-06
118 commits to master branch, last one about a year ago
174
219
mit
137
A single-cell RNAseq pipeline for 10X genomics data
Created 2019-04-08
1,612 commits to master branch, last one 14 days ago
24
192
gpl-3.0
7
Reference-guided transcript discovery and quantification for long read RNA-Seq data
Created 2020-02-07
2,159 commits to devel branch, last one 2 months ago
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
Created 2019-02-18
828 commits to devel branch, last one 7 months ago
15
175
bsd-3-clause
9
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
Created 2020-07-15
835 commits to master branch, last one a day ago
84
162
bsd-2-clause
13
RNA velocity estimation in Python
Created 2017-10-17
303 commits to master branch, last one 5 years ago
32
161
mit
16
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
Created 2017-09-15
653 commits to master branch, last one 18 days ago
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
Created 2019-07-11
1,483 commits to master branch, last one 10 months ago
14
154
other
13
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Created 2020-04-15
1,398 commits to master branch, last one 22 days ago
19
150
other
11
Fast, efficient RNA-Seq metrics for quality control and process optimization
Created 2017-08-10
410 commits to master branch, last one about a month ago
52
148
bsd-3-clause
8
Python library to access Gene Expression Omnibus Database (GEO)
Created 2015-08-16
238 commits to master branch, last one 8 months ago
98
147
mit
150
RNA-seq analysis pipeline for detection of gene-fusions
Created 2018-10-05
1,912 commits to master branch, last one 8 months ago
27
146
bsd-3-clause
7
Sequana: a set of Snakemake NGS pipelines
Created 2016-03-07
6,389 commits to main branch, last one 2 months ago