Alternatives and similar repositories for fastISM

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

• ebi-gene-expression-group / scanpy-scripts
  Scripts for using scanpy
  ☆38Updated last month
• shwhalen / ml-pitfalls
  Notebooks accompanying the paper "Navigating the pitfalls of applying machine learning in genomics"
  ☆46Updated 2 years ago
• MiraldiLab / maxATAC
  Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
  ☆29Updated 3 weeks ago
• ML4GLand / EUGENe
  Elucidating the Utility of Genomic Elements with Neural Nets
  ☆70Updated last year
• urmi-21 / pyrpipe
  Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
  ☆84Updated 4 years ago
• Maarten-vd-Sande / qnorm
  Fast-ish (and correct!) quantile normalization in Python.
  ☆31Updated 6 months ago
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆71Updated 2 years ago
• rajewsky-lab / spacemake
  ☆48Updated last week
• daisybio / NEASE
  A network-based approach for exon set enrichment
  ☆15Updated 4 months ago
• LieberInstitute / INTERACT
  ☆10Updated 3 years ago
• shtoneyan / gopher
  Toolset for training quantitative sequence to function models.
  ☆23Updated last year
• PMBio / deepcpg
  Deep neural networks for predicting CpG methylation
  ☆37Updated 8 years ago
• kundajelab / alzheimers_parkinsons
  Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis
  ☆46Updated 5 years ago
• aertslab / GENIE3
  GENIE3 (GEne Network Inference with Ensemble of trees) R-package
  ☆37Updated 3 years ago
• Papatheodorou-Group / BENGAL
  Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets
  ☆41Updated 4 months ago
• frankligy / SNAF
  Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing da…
  ☆51Updated 10 months ago
• aertslab / arboreto
  A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
  ☆63Updated last year
• umccr / neoantigens
  🏺 Exploring novel tumor epitope identification
  ☆37Updated 5 years ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆66Updated 5 months ago
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆32Updated 10 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
  ☆56Updated last year
• devCellPy-Team / devCellPy
  devCellPy is a Python package designed for hierarchical multilayered classification of cells based on single-cell RNA-sequencing.
  ☆27Updated last year
• Christensen-Lab-Dartmouth / MethylNet
  Modular framework for deep learning predictions on methylation data.
  ☆55Updated 5 years ago
• lhqing / mouse_brain_2020
  Jupyter notebook repository for reproducing analysis in "DNA Methylation Landscape of the Mouse Brain at Single-Cell Resolution"
  ☆14Updated 5 years ago
• smaslova / AI-TAC
  ☆27Updated 2 years ago
• EngreitzLab / scE2G
  Pipeline to run scE2G
  ☆31Updated last month
• ylab-hi / ScanNeo
  A pipeline for identifying indel derived neoantigens using RNA-Seq data
  ☆30Updated 3 years ago
• theislab / sfaira
  data and model repository for single-cell data
  ☆136Updated last year
• YosefLab / Cassiopeia
  A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
  ☆96Updated last week
• minoda-lab / universc
  UniverSC: a flexible cross-platform single-cell data processing pipeline
  ☆46Updated last year