Alternatives and similar repositories for CREsted

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

• jmschrei / dragonnfruit
  A method for analyzing scATAC-seq experiments.
  ☆34Updated 6 months ago
• EngreitzLab / scE2G
  Pipeline to run scE2G
  ☆32Updated 2 months ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆41Updated 11 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆126Updated last month
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆58Updated this week
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆30Updated last week
• ajaynadig / TRADEtools
  ☆35Updated 9 months ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆78Updated last week
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆113Updated last year
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated 8 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆67Updated 5 months ago
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆34Updated 9 months ago
• cantinilab / Circe
  Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.
  ☆31Updated last month
• lcmmichielsen / scHPL
  ☆37Updated 9 months ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆53Updated 2 months ago
• HYsxe / PRINT
  ☆37Updated last year
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆32Updated 2 years ago
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆95Updated 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
• mostafavilabuw / EnformerAssessment
  ☆25Updated last year
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆56Updated last year
• josephreplogle / guide_calling
  Tools for sgRNA calling in direct capture Perturb-seq data
  ☆39Updated 2 years ago
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆42Updated 2 weeks ago
• Papatheodorou-Group / BENGAL
  Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets
  ☆41Updated 5 months ago
• BorchLab / Trex
  Using TCR and expression for sequence embedding
  ☆60Updated 4 months ago
• gifford-lab / prescient
  Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
  ☆51Updated 11 months ago
• yal054 / epiformer
  ☆26Updated 8 months ago
• buenrostrolab / scPrinter
  ☆56Updated 2 weeks ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆44Updated 3 months ago
• zhoujt1994 / scHiCluster
  ☆69Updated last month