Alternatives and similar repositories for ExPecto:

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

• sidhomj / DeepTCR
  Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
  ☆115Updated last year
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆95Updated 2 years ago
• kundajelab / bpnet
  Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
  ☆147Updated 5 months ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆134Updated last week
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆210Updated this week
• phbradley / tcr-dist
  Software tools for the analysis of epitope-specific T cell receptor (TCR) repertoires (scroll down for the README)
  ☆79Updated 3 years ago
• kundajelab / tfmodisco
  TF MOtif Discovery from Importance SCOres
  ☆132Updated 11 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆93Updated 2 months ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆222Updated 5 months ago
• Xinglab / DARTS
  Deep-learning Augmented RNA-seq analysis of Transcript Splicing
  ☆110Updated 11 months ago
• mikessh / vdjtools
  [REPLACED by https://github.com/antigenomics/mirpy] Post-analysis of immune repertoire sequencing data
  ☆133Updated 7 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆68Updated 6 months ago
• r-bioinformatics / edgePy
  A Python implementation of edgeR for differential expression analysis
  ☆97Updated 5 years ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆141Updated 10 months ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆179Updated 4 years ago
• broadinstitute / depmap_omics
  What you need to process the Quarterly DepMap-Omics releases from Terra
  ☆114Updated 2 weeks ago
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆216Updated last month
• immunoengineer / gliph
  Grouping of Lymphocyte Interactions by Paratope Hotspots
  ☆90Updated 4 years 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
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated 8 months ago
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆184Updated 2 years ago
• urmi-21 / pyrpipe
  Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
  ☆82Updated 3 years ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆87Updated 5 years ago
• Illumina / PrimateAI
  deep residual neural network for classifying the pathogenicity of missense mutations.
  ☆114Updated 3 years ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆223Updated this week
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆192Updated 9 months ago
• wckdouglas / diffexpr
  Porting DESeq2 into python via rpy2
  ☆68Updated last year
• KrishnaswamyLab / SingleCellWorkshop
  ☆91Updated 3 years ago
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆95Updated 11 months ago
• broadinstitute / ichorCNA
  Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
  ☆171Updated 9 months ago