swainasish

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

ArchRtoSignac

An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)

ENGEP

shinylive-r

A guide for deploying Shinylive R application into Github Pages

r-shinylive-demo

Deploying an R Shiny Application in Quarto with Shinylive (No Shiny Server Required)

admultiregion_analysis

Code repository for single-cell atlas of Alzheimer's disease progression across brain regions

nichenetr

NicheNet: predict active ligand-target links between interacting cells

STALocator

mergelanes

Merge fastq files split over lanes

SpatialPrompt

spatially aware scalable and accurate tool for spot deconvolution and clustering in spatial transcriptomics

spatialID

ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

Cellcano

Supervised cell type identification for scATAC-seq data

ALU_IndiGen

An Indian population specific Alu insertion map

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

puter

🌐 The Internet OS! Free, Open-Source, and Self-Hostable.

xCell

Cell types enrichment analysis

paxmod

🕊️ Firefox add-on for multi-row tabs and site-dependent tab colors

GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

MEGAnE

MEGAnE

Banksy

BANKSY: spatial clustering

SONAR

SONAR is the algorithm of cell-type deconvolution for spatial transcriptomics

cassowary

Run Windows Applications on Linux as if they are native, Use linux applications to launch files files located in windows vm without needing to install applications on vm. With easy to use configuration GUI

SoloTE

scTE

distrobox

Use any linux distribution inside your terminal. Enable both backward and forward compatibility with software and freedom to use whatever distribution you’re more comfortable with. Mirror available at: https://gitlab.com/89luca89/distrobox

liver_cancer_subtype

subtype analysis in Liver cancer using single cell transcriptomics

mkdocs-material

Documentation that simply works

harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

STAR

RNA-seq aligner