Alternatives and similar repositories for scDEF

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

• dawe / schist
  An interface for Nested Stochastic Block Model for single cell analysis
  ☆36Updated 2 months ago
• cbg-ethz / SCATrEx
  Map single-cell transcriptomes to copy number evolutionary trees.
  ☆13Updated last year
• scverse / genomic-features
  Genomic Features in Python from BioConductor's AnnotationHub
  ☆22Updated last week
• scverse / ecosystem-packages
  Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
  ☆27Updated last week
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆30Updated 2 years ago
• YosefLab / Cassiopeia
  A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
  ☆93Updated last month
• const-ae / pyLemur
  A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
  ☆26Updated 8 months ago
• cellarium-ai / cellarium-ml
  Distributed single-cell data analysis.
  ☆31Updated last week
• theislab / batchglm
  Fit generalized linear models in python.
  ☆28Updated 2 years ago
• jmschrei / dragonnfruit
  A method for analyzing scATAC-seq experiments.
  ☆34Updated 2 months ago
• saezlab / dorothea-py
  Dorothea package in Python
  ☆11Updated 3 years ago
• dissatisfaction-ai / scHierarchy
  A toolking for cell type hierarchies: marker selection & consistent classification
  ☆22Updated last year
• sfortma2 / scranPY
  A python implementation of scran computeSumFactors: normalization by deconvolution for single-cell RNA-sequencing
  ☆35Updated last year
• almaan / eggplant
  ☆22Updated 3 years ago
• gifford-lab / prescient
  Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
  ☆49Updated 7 months ago
• jkobject / scDataLoader
  a dataloader to work with large single cell datasets from lamindb
  ☆29Updated this week
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆60Updated last month
• calico / velodyn
  Dynamical systems methods for RNA velocity analysis
  ☆24Updated 4 years ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆42Updated 2 years ago
• cbg-ethz / BnpC
  Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates
  ☆20Updated last year
• aristoteleo / Scribe-py
  Regulatory networks with Direct Information in python
  ☆40Updated 2 years ago
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆29Updated last week
• Teichlab / MultiMAP
  MultiMAP for integration of single cell multi-omics
  ☆56Updated last year
• dpeerlab / scKINETICS
  Code for scKINETICS (ISMB 2023)
  ☆22Updated last year
• WangPeng-Lab / scGCO
  Single-cell Graph Cuts Optimization
  ☆16Updated last year
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆89Updated 10 months ago
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆99Updated 3 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
  ☆54Updated last year
• lilab-bcb / harmony-pytorch
  ☆55Updated 3 months ago
• jmbreda / Sanity
  Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
  ☆78Updated 4 months ago