Alternatives and similar repositories for notebooks

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

• single-cell-genetics / XClone
  Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.
  ☆38Updated 2 weeks ago
• UPSUTER / GEMLI
  ☆33Updated last year
• alexisvdb / singleCellHaystack
  Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
  ☆86Updated 2 months ago
• rajewsky-lab / spacemake
  ☆49Updated this week
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆56Updated 8 months ago
• cbg-ethz / SCICoNE
  Single-cell copy number calling and event history reconstruction.
  ☆28Updated last year
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 3 years ago
• jon-xu / scSplit
  Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples withi…
  ☆41Updated 3 years ago
• PoolLab / generecovery
  ☆29Updated 2 years ago
• dpeerlab / Harmony
  Harmony framework for connecting scRNA-seq data from discrete time points
  ☆53Updated 2 months ago
• JEFworks-Lab / veloviz
  RNA-velocity informed embeddings for visualizing cellular trajectories
  ☆44Updated 3 years ago
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆24Updated 2 years ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 3 years ago
• lhqing / cemba_data
  Mapping pipeline for snmC-seq based technologies.
  ☆20Updated 2 years ago
• Teichlab / snp2cell
  cell type specific, trait-associated gene regulation
  ☆29Updated 10 months ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆66Updated 2 years ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆48Updated 8 months ago
• jbergenstrahle / STUtility
  ☆53Updated 2 years ago
• Zhen-Miao / PICsnATAC
  Paired Insertion Counting for snATAC-seq data
  ☆19Updated 8 months ago
• frankligy / scTriangulate
  scTriangulate is a Python package to mix-and-match conflicting clustering results in single cell analysis and generate reconciled cluster…
  ☆37Updated 2 years ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆58Updated 4 years ago
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆68Updated 6 years ago
• cole-trapnell-lab / cicero-release
  ☆59Updated last year
• kharchenkolab / cacoa
  Single-cell Case Control Analysis
  ☆52Updated last week
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆44Updated 5 years ago
• colomemaria / epiAneufinder
  R package to detect breakpoints and assign somies to scATAC-seq data
  ☆42Updated 2 months 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
  ☆57Updated last year
• nghiavtr / SCmut
  ☆34Updated 6 years ago
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆46Updated 5 months ago