13 results found Sort:

owkin
PyDESeq2 owkin
71
619
mit
11
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
python rna-seq bioinformatics transcriptomics differential-expression
Created 2022-11-22
337 commits to main branch, last one 12 days ago
dmcable
spacexr dmcable
75
331
gpl-3.0
10
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
differential-expression spatial-transcriptomics cell-type-identification
Created 2020-02-06
331 commits to master branch, last one 11 months ago
theislab
diffxpy theislab
23
195
bsd-3-clause
7
Differential expression analysis for single-cell RNA-seq data.
tensorflow bioinformatics transcriptomics gene-set-enrichment single-cell-rna-seq differential-expression
Created 2018-07-02
478 commits to master branch, last one about a year ago
stemangiola
tidybulk stemangiola
25
166
unknown
6
Brings bulk and pseudobulk transcriptomics to the tidyverse
pca gsea pipe tidy tsne edger deseq2 entrez tibble tidy-data tidyverse redundancy ensembl-ids transcripts bioconductor gene-symbols mds-dimensions transcriptomics differential-expression bulk-transcriptional-analyses
Created 2019-08-28
1,483 commits to master branch, last one about a month ago
saeyslab
multinichenetr saeyslab
15
135
gpl-3.0
3
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
scrna-seq single-cell ligand-target ligand-receptor systems-biology single-cell-rna-seq cell-cell-interaction cell-cell-communication differential-expression intercellular-signaling intercellular-communication ligand-receptor-interaction
Created 2021-02-16
137 commits to main branch, last one 19 days ago
parashardhapola
scarf parashardhapola
12
99
bsd-3-clause
5
Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
tsne umap big-data cite-seq genomics scrna-seq clustering multiomics pseudotime scatac-seq gene-modules bioinformatics graph-analytics memory-efficient dimension-reduction single-cell-rna-seq single-cell-atac-seq single-cell-genomics scalable-data-analysis differential-expression
Created 2020-05-07
1,026 commits to master branch, last one 13 days ago
nf-core
differentialabundance nf-core
42
72
mit
149
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
gsea limma shiny deseq2 nf-core rna-seq atac-seq chip-seq nextflow pipeline workflow microarray differential-abundance differential-expression
Created 2022-10-12
1,105 commits to master branch, last one 9 months ago
wckdouglas
diffexpr wckdouglas
21
68
mit
2
Porting DESeq2 into python via rpy2
python rna-seq differential-expression
Created 2018-03-24
170 commits to master branch, last one about a year ago
jackbibby1
SCPA jackbibby1
6
67
gpl-3.0
2
R package for pathway analysis in scRNA-seq data
r-package single-cell gene-signatures transcriptomics pathway-analysis single-cell-rna-seq differential-expression
Created 2021-11-16
449 commits to main branch, last one 8 months ago
snakemake-workflows
rna-seq-kallisto-sleuth snakemake-workflows
46
66
mit
5
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
sleuth rna-seq kallisto snakemake sciworkflows reproducibility differential-expression
Created 2018-12-12
173 commits to main branch, last one 10 days ago
Russel88
DAtest Russel88
9
50
gpl-3.0
8
Compare different differential abundance and expression methods
16s auc otu rnaseq microbiome proteomics metabolomics metagenomics compare-methods relative-abundances marker-gene-analysis false-positive-control differential-expression differential-abundance-methods
Created 2017-06-23
214 commits to master branch, last one 2 years ago
heiniglab
scPower heiniglab
5
45
unknown
2
Experimental design framework for scRNAseq population studies (eQTL and DE)
eqtl single-cell power-analysis differential-expression
Created 2020-03-24
113 commits to master branch, last one 25 days ago
grimmlab
BookChapter-RNA-Seq-Analyses grimmlab
10
40
gpl-3.0
4
Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis
pipeline bioinformatics rnaseq-analysis differential-expression
Created 2020-03-02
114 commits to master branch, last one 3 years ago