Alternatives and similar repositories for BENGI

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

• EngreitzLab / ABC-GWAS-Paper
  Code to reproduce analyses in Nasser, Bergman, Fulco, Guckelberger, Doughty et al Nature 2021
  ☆15Updated 4 years ago
• broadinstitute / single_cell_classification
  Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles
  ☆29Updated 5 years ago
• WeiqiangZhou / BIRD
  Big data Regression for predicting DNase I hypersensitivity
  ☆30Updated 9 months ago
• liulab-dfci / lisa2
  ☆30Updated 2 years ago
• josephreplogle / guide_calling
  Tools for sgRNA calling in direct capture Perturb-seq data
  ☆35Updated 2 years ago
• SUwonglab / PECA
  PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
  ☆43Updated last year
• PMBio / scNMT-seq
  single-cell Nucleosome Methylation Transcription
  ☆13Updated 7 years ago
• GuanLab / Anchor
  This is the package of Yuanfang's winning algorithm in the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge
  ☆20Updated 5 years ago
• wenweixiong / MARVEL
  ☆49Updated 10 months ago
• cboix / EPIMAP_ANALYSIS
  Epimap processing and analysis code repository
  ☆33Updated 2 years ago
• GreenleafLab / chromVARmotifs
  R package with motifs for use with chromVAR
  ☆28Updated 7 years ago
• dbrg77 / scATAC_snakemake
  Snakemake pipeline for plate scATAC-seq processing
  ☆26Updated last year
• FunctionLab / sei-manuscript
  Code for reproducing the Sei manuscript results
  ☆17Updated 3 years ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• wanglabtongji / SCRIP
  SCRIP(Single Cell Regulatory network Inference using ChIP-seq) is a tool for evaluating the binding enrichment of specific TR at single-c…
  ☆20Updated 11 months ago
• tinglab / reCAT
  ☆20Updated 6 years ago
• Zhang-lab / BeCorrect
  ☆15Updated 4 years ago
• tianshilu / QBRC-Neoantigen-Pipeline
  QBRC Neoantigen calling pipeline with CSiN calculation embedded
  ☆24Updated 3 years ago
• tanlabcode / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆24Updated 9 months ago
• juliaolivieri / SpliZ_pipeline
  Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis
  ☆33Updated 3 years ago
• andrewrech / antigen.garnish
  ☆48Updated 2 years ago
• JiaqiLiZju / Nvwa
  ☆34Updated 2 years ago
• MiraldiLab / maxATAC
  Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
  ☆28Updated 2 months ago
• sajuukLyu / Guan_et_al._2022
  ☆11Updated 2 years ago
• wangjuan001 / hicplus
  ☆11Updated 3 years ago
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated last year
• r3fang / snATAC
  <<------ Use SnapATAC!!
  ☆25Updated 6 years ago
• yal054 / epiformer
  ☆26Updated 2 months ago
• ma-compbio / scGHOST
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment
  ☆20Updated last year
• weililab / scMAGeCK
  The R Bioconductor package for scMAGeCK.
  ☆13Updated last year