Alternatives and similar repositories for tfmodisco:

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

• kundajelab / bpnet
  Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
  ☆147Updated 5 months ago
• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆123Updated 4 years ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆134Updated last week
• kipoi / models
  Model zoo for genomics
  ☆167Updated 5 months ago
• kipoi / kipoiseq
  Standard set of data-loaders for training and making predictions for DNA sequence-based models.
  ☆81Updated 4 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆64Updated 6 months ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆222Updated 5 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆93Updated 2 months ago
• jmschrei / tangermeme
  Biological sequence analysis for the modern age.
  ☆205Updated last month
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆68Updated 6 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆95Updated 2 years ago
• kundajelab / ChromDragoNN
  Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellula…
  ☆44Updated 3 years ago
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆113Updated last month
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆210Updated this week
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆141Updated 10 months ago
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆179Updated 3 months ago
• Illumina / PrimateAI
  deep residual neural network for classifying the pathogenicity of missense mutations.
  ☆114Updated 3 years ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆87Updated 5 years ago
• urmi-21 / pyrpipe
  Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
  ☆82Updated 3 years ago
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆216Updated last month
• r-bioinformatics / edgePy
  A Python implementation of edgeR for differential expression analysis
  ☆97Updated 5 years ago
• kundajelab / ENCODE_downloader
  Downloader for ENCODE
  ☆31Updated 4 years ago
• GangCaoLab / CoolBox
  Jupyter notebook based genomic data visualization toolkit.
  ☆231Updated 6 months ago
• hms-dbmi / hic-data-analysis-bootcamp
  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
  ☆193Updated 6 years ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆179Updated 4 years ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆116Updated 2 years ago
• sidhomj / DeepTCR
  Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
  ☆115Updated last year
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆223Updated this week
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆135Updated 9 months ago
• open2c / cooltools
  The tools for your .cool's
  ☆143Updated 2 months ago