Alternatives and similar repositories for scanorama

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

• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆258Updated last month
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆321Updated 2 years ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆366Updated 4 months ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 5 years ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆234Updated 2 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆169Updated last year
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆218Updated 2 years ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆302Updated last month
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆311Updated 5 years ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆295Updated 2 years ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆299Updated 3 years ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆226Updated last year
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆168Updated 2 years ago
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆174Updated last month
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆205Updated last month
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆300Updated 3 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆448Updated last year
• IanevskiAleksandr / sc-type
  ☆277Updated last year
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆161Updated 4 years ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆194Updated 2 years ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆420Updated last month
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆224Updated last year
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆229Updated this week
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆355Updated this week
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆239Updated 10 months ago
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆301Updated last week
• xuranw / MuSiC
  Multi-subject Single Cell Deconvolution
  ☆276Updated last year
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆242Updated last week
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆189Updated 3 years ago
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆209Updated 2 years ago