Alternatives and similar repositories for single-cell-best-practices

Users that are interested in single-cell-best-practices are comparing it to the libraries listed below

• theislab / single-cell-tutorial
  Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…
  ☆1,509Updated 2 years ago
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆733Updated last week
• hbctraining / Intro-to-scRNAseq
  ☆622Updated 5 months ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆442Updated 9 months ago
• Starlitnightly / omicverse
  A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
  ☆733Updated last week
• pachterlab / BI-BE-CS-183-2023
  Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023
  ☆500Updated last year
• hbctraining / scRNA-seq
  ☆580Updated 4 years ago
• mikelove / awesome-multi-omics
  List of software packages for multi-omics analysis
  ☆834Updated this week
• crazyhottommy / scRNAseq-analysis-notes
  scRNAseq analysis notes from Ming Tang
  ☆736Updated 9 months ago
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆654Updated last week
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆538Updated 2 months ago
• hemberg-lab / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆675Updated 3 years ago
• sqjin / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
  ☆726Updated last year
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆566Updated last month
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆1,036Updated 3 years ago
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆636Updated 7 months ago
• scverse / scvi-tools
  Deep probabilistic analysis of single-cell and spatial omics data
  ☆1,449Updated this week
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆464Updated 6 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆460Updated 2 weeks ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆379Updated 8 months ago
• owkin / PyDESeq2
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
  ☆676Updated last week
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆597Updated this week
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆430Updated 3 months ago
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆428Updated this week
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆477Updated 4 months ago
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆818Updated last year
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆473Updated 2 weeks ago
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆428Updated 7 months ago
• gao-lab / Guideline-for-Computational-Biology-and-Bioinformatics
  ☆356Updated 4 months ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆493Updated 5 months ago