Alternatives and similar repositories for scanpy-scripts

Users that are interested in scanpy-scripts are comparing it to the libraries listed below

• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆76Updated 2 years ago
• dpeerlab / Harmony
  Harmony framework for connecting scRNA-seq data from discrete time points
  ☆51Updated last year
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆42Updated 2 months ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆57Updated 4 years ago
• minoda-lab / universc
  UniverSC: a flexible cross-platform single-cell data processing pipeline
  ☆46Updated last year
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• cole-trapnell-lab / cicero-release
  ☆58Updated last year
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆32Updated 3 years ago
• lcmmichielsen / scHPL
  ☆37Updated 7 months ago
• hemberg-lab / scfind
  ☆43Updated 2 years ago
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆55Updated last year
• neurorestore / DE-analysis
  ☆39Updated 4 years ago
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆55Updated 4 years ago
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆45Updated 5 years ago
• rargelaguet / scnmt_gastrulation
  scNMT-seq gastrulation
  ☆42Updated 2 years ago
• HYsxe / PRINT
  ☆36Updated last year
• morris-lab / Capybara
  Capybara: A computational tool to measure cell identity and fate transitions
  ☆59Updated 3 years ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 2 years ago
• single-cell-genetics / vireo
  Demultiplexing pooled scRNA-seq data with or without genotype reference
  ☆87Updated 6 months ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆89Updated 5 months ago
• alexisvdb / singleCellHaystack
  Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
  ☆85Updated last year
• KenLauLab / dropkick
  Automated cell filtering for single-cell RNA sequencing data
  ☆25Updated last year
• qinqian / lisa
  epigenome analysis to rank transcription factors
  ☆31Updated 2 years ago
• krasnowlab / HLCA
  ☆60Updated 4 years ago
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆79Updated 7 months ago
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆89Updated last year
• JunyueC / sci-fate_analysis
  Downstream analysis script for sci-fate (TF-gene linkage analysis / cell linkage analysis)
  ☆24Updated 5 years ago
• gofflab / developing_mouse_retina_scRNASeq
  10x single cell RNA-seq data from the developing mouse retina
  ☆16Updated 4 years ago
• theislab / pseudodynamics
  Dynamic models for single-cell RNA-seq time series.
  ☆40Updated 7 years ago
• jdekanter / CHETAH
  scRNA-seq cell type identification
  ☆43Updated 6 years ago