fastq utilsValidation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
Stars: ✭ 25 (-59.68%)
alevin-fry🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
Stars: ✭ 78 (+25.81%)
SCICoNESingle-cell copy number calling and event history reconstruction.
Stars: ✭ 20 (-67.74%)
NGSNext-Gen Sequencing tools from the Horvath Lab
Stars: ✭ 30 (-51.61%)
dyngenSimulating single-cell data using gene regulatory networks 📠
Stars: ✭ 59 (-4.84%)
scAlignA deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches
Stars: ✭ 32 (-48.39%)
SCopeFast visualization tool for large-scale and high dimensional single-cell data
Stars: ✭ 62 (+0%)
scATAC-proA comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
Stars: ✭ 63 (+1.61%)
ExpressionMatrix2Software for exploration of gene expression data from single-cell RNA sequencing.
Stars: ✭ 29 (-53.23%)
CrossTalkeRR package to do the Ligand Receptor Analysis Visualization
Stars: ✭ 33 (-46.77%)
cardelinoClone identification from single-cell data
Stars: ✭ 49 (-20.97%)
Awesome Single CellCommunity-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Stars: ✭ 1,937 (+3024.19%)
scPowerExperimental design framework for scRNAseq population studies (eQTL and DE)
Stars: ✭ 19 (-69.35%)
velodynDynamical systems methods for RNA velocity analysis
Stars: ✭ 16 (-74.19%)
switchdeInference of switch-like differential expression along single-cell trajectories
Stars: ✭ 19 (-69.35%)
netSmoothnetSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
Stars: ✭ 23 (-62.9%)
babelDeep learning model for single-cell inference of multi-omic profiles from a single input modality.
Stars: ✭ 20 (-67.74%)
scarchesReference mapping for single-cell genomics
Stars: ✭ 175 (+182.26%)
cellSNPPileup biallelic SNPs from single-cell and bulk RNA-seq data
Stars: ✭ 42 (-32.26%)
dbMAPA fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.
Stars: ✭ 39 (-37.1%)
kmer-homology-paperManuscript for functional prediction of transcriptomic “dark matter” across species
Stars: ✭ 12 (-80.65%)
EWCEExpression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
Stars: ✭ 30 (-51.61%)
scABCNo description or website provided.
Stars: ✭ 16 (-74.19%)
EDS💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format
Stars: ✭ 16 (-74.19%)
SpiceMixspatial transcriptome, single cell
Stars: ✭ 19 (-69.35%)
MERINGUEcharacterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
Stars: ✭ 33 (-46.77%)
iDEADifferential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
Stars: ✭ 23 (-62.9%)
scDblFinderMethods for detecting doublets in single-cell sequencing data
Stars: ✭ 48 (-22.58%)
mgatkmgatk: mitochondrial genome analysis toolkit
Stars: ✭ 65 (+4.84%)
PandoMultiome GRN inference.
Stars: ✭ 21 (-66.13%)
crop-seqData analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)
Stars: ✭ 24 (-61.29%)
vitessceRR API and htmlwidget for Vitessce
Stars: ✭ 19 (-69.35%)
gchromVARCell type specific enrichments using finemapped variants and quantitative epigenetic data
Stars: ✭ 31 (-50%)
scCATCHAutomatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
Stars: ✭ 137 (+120.97%)
cellrangerRkitNon-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)
Stars: ✭ 18 (-70.97%)
cnaCovarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.
Stars: ✭ 35 (-43.55%)
immunarch🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
Stars: ✭ 204 (+229.03%)
GCModellerGCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language
Stars: ✭ 25 (-59.68%)
celltypistA tool for semi-automatic cell type annotation
Stars: ✭ 92 (+48.39%)
kallistobustoolskallisto | bustools workflow for pre-processing single-cell RNA-seq data
Stars: ✭ 79 (+27.42%)
SCopeLoomRR package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
Stars: ✭ 25 (-59.68%)
VoxHuntVoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps
Stars: ✭ 27 (-56.45%)
GLUEGraph-linked unified embedding for single-cell multi-omics data integration
Stars: ✭ 180 (+190.32%)
bapBead-based single-cell atac processing
Stars: ✭ 20 (-67.74%)
SCOPE-toolsSingle-Cell Omics Preparation Entity Tools
Stars: ✭ 14 (-77.42%)
CUT-RUNTools-2.0CUT&RUN and CUT&Tag data processing and analysis
Stars: ✭ 36 (-41.94%)
cellsnp-liteEfficient genotyping bi-allelic SNPs on single cells
Stars: ✭ 47 (-24.19%)
sintoTools for single-cell data processing
Stars: ✭ 74 (+19.35%)
anndata2riConvert between AnnData and SingleCellExperiment
Stars: ✭ 79 (+27.42%)
scMCAMouse cell atlas
Stars: ✭ 45 (-27.42%)
kanaSingle cell analysis in the browser
Stars: ✭ 81 (+30.65%)
NebulosaR package to visualize gene expression data based on weighted kernel density estimation
Stars: ✭ 50 (-19.35%)
trVAEConditional out-of-distribution prediction
Stars: ✭ 47 (-24.19%)