Alternatives and similar repositories for deepsea

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

• gagneurlab / MMSplice_MTSplice
  Tissue-specific variant effect predictions on splicing
  ☆42Updated 2 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
• PMBio / deepcpg
  Deep neural networks for predicting CpG methylation
  ☆37Updated 8 years ago
• zhangyan32 / HiCPlus
  ☆31Updated 6 years 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
• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆132Updated 9 months ago
• Xinglab / DARTS
  Deep-learning Augmented RNA-seq analysis of Transcript Splicing
  ☆115Updated last year
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 years ago
• Dongwon-Lee / lsgkm
  ☆51Updated last year
• kipoi / kipoiseq
  Standard set of data-loaders for training and making predictions for DNA sequence-based models.
  ☆82Updated last year
• wanwenzeng / ep2vec
  ☆22Updated 8 years ago
• kundajelab / tfmodisco
  TF MOtif Discovery from Importance SCOres
  ☆155Updated 3 weeks ago
• vagarwal87 / saluki_paper
  Saluki, a method to predict mRNA half-lives from sequence
  ☆25Updated 3 years ago
• uci-cbcl / FactorNet
  A deep learning package for predicting TF binding
  ☆42Updated 5 years ago
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆70Updated 2 years ago
• ucscXena / xenaPython
  Python API for Xena Hub
  ☆53Updated 2 years ago
• vagarwal87 / Xpresso
  Predicting gene expression levels from genomic sequences
  ☆54Updated 5 years ago
• SUwonglab / PECA
  PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
  ☆45Updated 3 weeks ago
• ohlerlab / DeepRiPe
  ☆24Updated last year
• XWangLabTHU / cfDNApipe
  cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
  ☆71Updated 3 years ago
• openvax / gtfparse
  Parsing tools for GTF (gene transfer format) files
  ☆121Updated 8 months ago
• kircherlab / CADD-scripts
  CADD scripts release for offline scoring. For more information about CADD, please visit our website
  ☆87Updated last week
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆85Updated last month
• 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
• ICGC-TCGA-PanCancer / TumorType-WGS
  Classifying tumor types based on Whole Genome Sequencing (WGS) data
  ☆48Updated last year
• kundajelab / dfim
  Deep Feature Interaction Maps (DFIM)
  ☆54Updated 6 years ago
• shwhalen / targetfinder
  ☆84Updated 4 years ago
• openvax / neoantigen-vaccine-pipeline
  Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines
  ☆86Updated last month
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆30Updated 9 months ago
• johli / aparent
  APA Regression Net - Predict and Engineer Alternative Polyadenylation
  ☆39Updated 4 years ago