alperoglu's Stars
alshedivat/al-folio
A beautiful, simple, clean, and responsive Jekyll theme for academics
lmcinnes/umap
Uniform Manifold Approximation and Projection
crazyhottommy/RNA-seq-analysis
RNAseq analysis notes from Ming Tang
broadinstitute/infercnv
Inferring CNV from Single-Cell RNA-Seq
pachterlab/ffq
A tool to find sequencing data and metadata from public databases.
corybrunson/ggalluvial
ggplot2 extension for alluvial plots
therneau/survival
Survival package for R
dylkot/cNMF
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
broadinstitute/Tangram
Spatial alignment of single cell transcriptomic data.
ZJUFanLab/scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
navinlabcode/copykat
saezlab/liana
LIANA: a LIgand-receptor ANalysis frAmework
kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
davidsjoberg/ggstream
A package to make streamplots
saezlab/decoupler-py
Python package to perform enrichment analysis from omics data.
neurorestore/Libra
icbi-lab/infercnvpy
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
JiekaiLab/scDIOR
scDIOR: Single cell data IO softwaRe
single-cell-genetics/cellsnp-lite
Efficient genotyping bi-allelic SNPs on single cells
digitalcytometry/cytospace
CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
Swarbricklab-code/BrCa_cell_atlas
Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".
navinlabcode/CellTrek
neurorestore/Augur
Cell type prioritization in single-cell data
Teichlab/cellhint
A tool for semi-automatic cell type harmonization and integration
theislab/cpa
The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.
kbroman/qtl
R/qtl: A QTL mapping environment
ShellyCoder/cellcall
inferring cell-cell communication from scRNA-seq of ligand-receptor
ma-compbio/SpiceMix
spatial transcriptome, single cell
RTCGA/RTCGA
Download, integration and visualizations of the variety & volume of TCGA data.
theislab/scTab