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
• broadinstitute / Drop-seq
  Java tools for analyzing Drop-seq data
  ☆128Updated this week
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆171Updated last month
• Hoohm / dropSeqPipe
  A SingleCell RNASeq pre-processing snakemake workflow
  ☆149Updated 2 years ago
• JonathanShor / DoubletDetection
  Doublet detection in single-cell RNA-seq data.
  ☆91Updated 4 months ago
• timoast / sinto
  Tools for single-cell data processing
  ☆125Updated last year
• kharchenkolab / dropEst
  Pipeline for initial analysis of droplet-based single-cell RNA-seq data
  ☆91Updated 3 years ago
• 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…
  ☆106Updated 2 years ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆101Updated last year
• Teichlab / tracer
  TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
  ☆130Updated last year
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆90Updated 5 years ago
• AllonKleinLab / SPRING
  ☆68Updated 7 years ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated 2 years ago
• scverse / scanpy_usage
  Scanpy use cases.
  ☆85Updated 4 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆162Updated last year
• aertslab / SCope
  Fast visualization tool for large-scale and high dimensional single-cell data
  ☆74Updated 2 years ago
• TrinityCTAT / Trinity_CTAT
  ☆117Updated last year
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆192Updated 2 years ago
• mohuangx / SAVER
  Single-cell RNA-seq Gene Expression Recovery
  ☆109Updated 6 months ago
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆112Updated 7 months ago
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆109Updated 7 months ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆178Updated 11 months ago
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆68Updated 5 years ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 3 years ago
• jmbreda / Sanity
  Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
  ☆76Updated last month
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆96Updated 4 years ago
• farrellja / URD
  URD - Reconstruction of Branching Developmental Trajectories
  ☆124Updated 3 years ago
• broadinstitute / single_cell_portal
  Tutorials, workflows, and convenience scripts for Single Cell Portal
  ☆50Updated last year
• csoneson / conquer_comparison
  Code for evaluation of differential expression methods in single-cell RNA-seq data
  ☆112Updated 4 years ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 2 months ago