theislab / diffxpy

Related projects ⓘ

Alternatives and complementary repositories for diffxpy

• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆141Updated 6 months ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆177Updated 3 years ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆138Updated 3 years ago
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆161Updated last month
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆292Updated 5 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆295Updated 3 months ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆219Updated this week
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆137Updated this week
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆167Updated last month
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆154Updated 9 months ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆183Updated 7 months ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆217Updated last week
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆145Updated 6 months ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆187Updated last year
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆182Updated 2 months ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆145Updated 4 months ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆143Updated last year
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆131Updated 2 years ago
• liulab-dfci / TRUST4
  TCR and BCR assembly from RNA-seq data
  ☆278Updated this week
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆132Updated 2 years ago
• Dragonmasterx87 / Interactive-3D-Plotting-in-Seurat-3.0.0
  This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data
  ☆116Updated last year
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆277Updated last year
• dviraran / xCell
  Cell types enrichment analysis
  ☆182Updated 5 months ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆306Updated last year
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆150Updated 2 weeks ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆272Updated 2 months ago
• kaizhang / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆228Updated last week
• kharchenkolab / pagoda2
  R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
  ☆210Updated 8 months ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆250Updated last month
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆150Updated last year