Alternatives and similar repositories for scRNAseq_Benchmark

Users that are interested in scRNAseq_Benchmark are comparing it to the libraries listed below

• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 4 years ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆192Updated 2 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆167Updated last year
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆166Updated 2 years ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆212Updated last year
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆141Updated last year
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆291Updated 2 years ago
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆132Updated last year
• dviraran / xCell
  Cell types enrichment analysis
  ☆200Updated last year
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆181Updated last year
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆205Updated 2 years ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆210Updated last year
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆231Updated 2 years ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆318Updated 2 years ago
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆214Updated last year
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆146Updated 3 years ago
• tallulandrews / scRNASeqPipeline
  ☆118Updated 7 years ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆138Updated 2 years ago
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆139Updated 3 years ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆150Updated last year
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆172Updated 4 months ago
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆189Updated 10 months 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
  ☆121Updated 2 years ago
• navinlabcode / copykat
  ☆250Updated last year
• mdozmorov / scATAC-seq_notes
  scATAC-seq data analysis tools and papers
  ☆120Updated 2 months ago
• farrellja / URD
  URD - Reconstruction of Branching Developmental Trajectories
  ☆124Updated 4 years ago
• zhangyuqing / ComBat-seq
  Batch effect adjustment based on negative binomial regression for RNA sequencing count data
  ☆192Updated 4 years ago
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆236Updated 2 months ago
• NBISweden / excelerate-scRNAseq
  Single RNA-seq data analysis with R (Finland, May, 2019)
  ☆225Updated 3 years ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆176Updated last year