Alternatives and similar repositories for crestree

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

• 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
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆62Updated last year
• quadbio / simspec
  Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)
  ☆35Updated last year
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆49Updated last year
• forrest-lab / NATMI
  NATMI: Network Analysis Toolkit for the Multicellular Interactions
  ☆35Updated 4 years ago
• kunwang34 / PhyloVelo
  PhyloVelo, Phylogeny-based transcriptomic velocity of single cells
  ☆43Updated 2 months ago
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆22Updated last year
• doraadong / TraSig
  Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data
  ☆25Updated 2 years ago
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆29Updated last year
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆77Updated 3 months ago
• WWXkenmo / ICAnet
  Independent Component Analysis decipher functional modules for better cell clustering and annotation
  ☆17Updated 3 years ago
• MagpiePKU / EpiTrace
  Cell age determination by scATAC-seq and bulk-ATAC-seq
  ☆32Updated last year
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆56Updated 6 months ago
• buenrostrolab / stimATAC_analyses_code
  All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs
  ☆41Updated 2 years ago
• gitter-lab / SINGE
  Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
  ☆11Updated last year
• FloWuenne / scFunctions
  Functions for single cell data analysis
  ☆32Updated 4 years ago
• morris-lab / BiddyetalWorkflow
  This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.
  ☆32Updated last year
• AllonKleinLab / cospar
  ☆26Updated last year
• KlugerLab / GeneTrajectory-python
  Python implementation of Gene Trajectory
  ☆30Updated last year
• veltenlab / CloneTracer
  This repository contains scripts to identify healthy and malignant cells from scRNAseq with CloneTracer and process data from Optimized 1…
  ☆26Updated last year
• caleblareau / mtscATACpaper_reproducibility
  Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020
  ☆18Updated 2 years ago
• mvinyard / ArchR-h5ad
  Parse ArchR arrow files to anndata h5ad
  ☆15Updated last year
• shyhihihi / MERCI
  MERCI for tracing of mitochondrion transfer between single cancer and T cells
  ☆24Updated last year
• aet21 / SCENT
  Estimation of Single-Cell Potency with Single Cell Entropy
  ☆43Updated 2 years ago
• dpeerlab / pdac-progression
  ☆10Updated 2 years ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆41Updated 10 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆66Updated 4 months ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 3 weeks ago
• mahmoudibrahim / genesorteR
  Feature Ranking in (possibly large) Clustered Single Cell Data
  ☆40Updated 4 years ago
• xichensf / magical
  R and MATLAB scripts for MAGICAL
  ☆11Updated last year