Alternatives and similar repositories for loompy:

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

• AllonMKlein / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆85Updated 5 years ago
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆164Updated last year
• aertslab / SCope
  Fast visualization tool for large-scale and high dimensional single-cell data
  ☆69Updated 2 years ago
• scverse / scanpy_usage
  Scanpy use cases.
  ☆82Updated 4 years ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated last year
• Teichlab / tracer
  TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
  ☆126Updated last year
• AllonKleinLab / SPRING
  ☆67Updated 6 years ago
• JonathanShor / DoubletDetection
  Doublet detection in single-cell RNA-seq data.
  ☆91Updated last month
• kharchenkolab / dropEst
  Pipeline for initial analysis of droplet-based single-cell RNA-seq data
  ☆91Updated 2 years ago
• broadinstitute / Drop-seq
  Java tools for analyzing Drop-seq data
  ☆125Updated last month
• BUStools / bustools
  Tools for working with BUS files
  ☆95Updated 5 months ago
• timoast / sinto
  Tools for single-cell data processing
  ☆122Updated 9 months ago
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• mohuangx / SAVER
  Single-cell RNA-seq Gene Expression Recovery
  ☆110Updated 3 months ago
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆108Updated 4 months ago
• YeoLab / single-cell-bioinformatics
  Course material in notebook format for learning about single cell bioinformatics methods
  ☆102Updated 8 years ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆142Updated 3 months ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆161Updated last year
• PMBio / scLVM
  scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources…
  ☆105Updated 2 years ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆61Updated last year
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆112Updated this week
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆95Updated 4 years ago
• jmbreda / Sanity
  Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
  ☆70Updated last year
• broadinstitute / single_cell_portal
  Tutorials, workflows, and convenience scripts for Single Cell Portal
  ☆50Updated last year
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆117Updated 2 years ago
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆106Updated 4 months ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆169Updated 8 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆158Updated last year
• AllonKleinLab / SPRING_dev
  ☆69Updated 11 months ago
• 10XGenomics / single-cell-3prime-paper
  ☆85Updated 4 years ago