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
  ☆154Updated 10 months ago
• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆127Updated 4 months ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆160Updated 3 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆78Updated last month
• kipoi / models
  Model zoo for genomics
  ☆166Updated 10 months ago
• jmschrei / tangermeme
  Biological sequence analysis for the modern age.
  ☆223Updated 3 weeks ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆231Updated 4 months ago
• kipoi / kipoiseq
  Standard set of data-loaders for training and making predictions for DNA sequence-based models.
  ☆81Updated 9 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆94Updated 3 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆75Updated 10 months ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆88Updated 5 years ago
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆230Updated 2 weeks ago
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆94Updated 6 months ago
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆97Updated 4 months ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 2 years ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆105Updated 2 years ago
• GangCaoLab / CoolBox
  Jupyter notebook based genomic data visualization toolkit.
  ☆237Updated last month
• 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
• open2c / cooltools
  The tools for your .cool's
  ☆151Updated 7 months ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆148Updated last year
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆191Updated 2 weeks ago
• Illumina / PrimateAI
  deep residual neural network for classifying the pathogenicity of missense mutations.
  ☆113Updated 3 years ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆183Updated 4 years ago
• r-bioinformatics / edgePy
  A Python implementation of edgeR for differential expression analysis
  ☆103Updated 6 years ago
• kundajelab / ENCODE_downloader
  Downloader for ENCODE
  ☆32Updated 4 years ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆200Updated this week
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆249Updated 6 months ago
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆83Updated 3 months ago
• mdozmorov / scHiC_notes
  Notes on single-cell Hi-C technologies, tools, and data
  ☆79Updated 7 months ago
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆223Updated last month