Alternatives and similar repositories for LineageOT

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

• matsengrp / gapml
  ☆11Updated 4 years ago
• AllonKleinLab / PBA
  Population balance analysis
  ☆44Updated 6 years ago
• jessica1338 / LinTIMaT
  Lineage Tracing by Integrating Mutation and Transcriptomic data
  ☆13Updated 5 years ago
• hmatsu1226 / SCODE
  SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
  ☆45Updated 5 years ago
• dpeerlab / scKINETICS
  Code for scKINETICS (ISMB 2023)
  ☆22Updated 2 years ago
• YosefLab / Cassiopeia
  A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
  ☆96Updated last week
• landau-lab / PATH
  ☆19Updated last year
• jessica1338 / CSHMM-for-time-series-scRNA-Seq
  This is the code release for paper Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data
  ☆22Updated 7 years ago
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆31Updated 2 years ago
• cbg-ethz / scIsoPrep
  Single-cell Iso Prep
  ☆17Updated 2 years ago
• cbg-ethz / SCICoNE
  Single-cell copy number calling and event history reconstruction.
  ☆27Updated 11 months ago
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆29Updated last week
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆22Updated last year
• cantinilab / HuMMuS
  Molecular interactions inference from single-cell multi-omics data
  ☆28Updated 3 weeks ago
• DeplanckeLab / ChromatinHD
  High-definition modeling of chromatin + transcriptomics data
  ☆25Updated 7 months ago
• jmschrei / dragonnfruit
  A method for analyzing scATAC-seq experiments.
  ☆34Updated 5 months ago
• gwlab-ca / scsnv
  scSNV Mapping tool for 10X Single Cell Data
  ☆25Updated last year
• pachterlab / CGCCP_2023
  scVI extension for unspliced RNA
  ☆16Updated 6 months ago
• dpeerlab / Harmony
  Harmony framework for connecting scRNA-seq data from discrete time points
  ☆51Updated last year
• HYsxe / PRINT
  ☆37Updated last year
• cole-trapnell-lab / Scribe
  Regulatory networks with Direct Information
  ☆17Updated 6 years ago
• Teichlab / gene2probe
  Pipeline for designing custom probes against human genes
  ☆19Updated last year
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆54Updated last year
• mcvickerlab / varCA
  Use an ensemble of variant callers to call variants from ATAC-seq data
  ☆23Updated 6 months ago
• lcmmichielsen / scHPL
  ☆37Updated 8 months ago
• aertslab / ScoMAP
  ScoMAP is an R package to spatially integrate single-cell omics data into virtual cells and infer enhancer-to-gene relationships.
  ☆27Updated 4 years ago
• UPSUTER / GEMLI
  ☆32Updated 9 months ago
• juliaolivieri / SpliZ_pipeline
  Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis
  ☆35Updated 3 years ago
• lhqing / ALLCools
  Toolkit for single-cell DNA methylation analysis.
  ☆43Updated last week
• theislab / pseudodynamics
  Dynamic models for single-cell RNA-seq time series.
  ☆40Updated 7 years ago