Alternatives and similar repositories for deepC

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

• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆111Updated 3 years ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆82Updated last year
• johli / aparent
  APA Regression Net - Predict and Engineer Alternative Polyadenylation
  ☆40Updated 4 years ago
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆91Updated 3 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆87Updated 4 months ago
• vagarwal87 / Xpresso
  Predicting gene expression levels from genomic sequences
  ☆54Updated 5 years ago
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆95Updated 11 months ago
• SUwonglab / PECA
  PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
  ☆45Updated 4 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…
  ☆72Updated 2 years ago
• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆132Updated last year
• JiaqiLiZju / Nvwa
  ☆36Updated 3 years ago
• weng-lab / BENGI
  ☆18Updated 3 years ago
• yal054 / epiformer
  ☆27Updated 9 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆100Updated 11 months ago
• kundajelab / ChromDragoNN
  Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellula…
  ☆44Updated 4 years ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆44Updated 3 weeks ago
• jsxlei / SCALE
  Single-cell ATAC-seq analysis via Latent feature Extraction
  ☆103Updated 2 years ago
• zhoujt1994 / scHiCluster
  ☆69Updated 2 months ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆54Updated 2 weeks ago
• josephreplogle / guide_calling
  Tools for sgRNA calling in direct capture Perturb-seq data
  ☆41Updated 2 years ago
• mhorlbeck / ScreenProcessing
  ☆69Updated 2 years ago
• MiraldiLab / maxATAC
  Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
  ☆30Updated 2 months ago
• VRam142 / combinatorialHiC
  Scripts + resources for analyzing combinatorial Hi-C data
  ☆32Updated 6 years ago
• xryanglab / RiboMiner
  a toolset for mining multi-dimensional features of the translatome with ribosome profiling data
  ☆18Updated 6 months ago
• bm2-lab / MUSIC
  model-based understanding of single-cell CRISPR screening
  ☆26Updated last year
• s175573 / DeepCAT
  Deep Learning Method to Identify Cancer Associated TCRs
  ☆46Updated 3 years ago
• vagarwal87 / saluki_paper
  Saluki, a method to predict mRNA half-lives from sequence
  ☆27Updated 3 years ago
• Illumina / PromoterAI
  ☆88Updated 2 months ago
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆100Updated 5 months ago
• gao-lab / Cell_BLAST
  A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
  ☆95Updated last year