Alexandru-Emil's Stars
NBISweden/workshop-epigenomics-RTDs
workshop website on readthedocs
mildpiggy/DEP2
An r package for proteomics data Analysis, developed from DEP.
gustaveroussy/sopa
Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
saezlab/DOT
DOT
nolanlab/vortex
VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:
nolanlab/TissueSchematics
Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"
snap-stanford/stellar
SGDDNB/translational_regulation
Detection of differential translated genes using Ribo-seq
CarvunisLab/iRibo
iRibo
nf-core/riboseq
Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
ftwkoopmans/msdap
MS-DAP: downstream analysis pipeline for quantitative proteomics
nf-core/quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
yuqiuzhou/Pianno
quon-titative-biology/scProjection
Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection
YangLabHKUST/SpatialScope
A unified approach for integrating spatial and single-cell transcriptomics data by leveraging deep generative models
tgirke/systemPipeR
Project Website:
ColemanRHarris/mxnorm
R package to normalize multiplexed imaging data.
systemPipeR/SPatacseq
Workflow Template
dmcable/spacexr
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
aicplane/Linkage
An R shiny web server for linking of ATAC-seq to gene expression data
satijalab/azimuth
A Shiny web app for mapping datasets using Seurat v4
C3BI-pasteur-fr/UTechSCB-SCHNAPPs
Shiny app for the analysis of single cell data
interactivereport/scRNAsequest
scRNASequest: an ecosystem of scRNA-seq analysis, visualization and publishing
seandavi/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
YosefLab/VISION
Signature Analysis and Visualization for Single-Cell RNA-seq
mdozmorov/scRNA-seq_notes
A list of scRNA-seq analysis tools
ncats/public_sequin
public production version of sequin to share with the public
morris-lab/CellOracle
This is the alpha version of the CellOracle package
theislab/scCODA
A Bayesian model for compositional single-cell data analysis
LewisLabUCSD/Celegans-cell2cell
Analyses for cell-cell interactions in C. elegans