kundajelab / bpnet
Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
☆150Updated 6 months ago
Alternatives and similar repositories for bpnet:
Users that are interested in bpnet are comparing it to the libraries listed below
- Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)☆140Updated last week
- TF MOtif Discovery from Importance SCOres☆133Updated last year
- A python extension for quick access to bigWig and bigBed files☆226Updated last month
- deep learning-inspired explainable sequence model for transcription initiation☆93Updated 3 months ago
- Biological sequence analysis for the modern age.☆207Updated 2 months ago
- predicting expression effects of human genome variants ab initio from sequence☆126Updated 3 weeks ago
- RNA-seq prediction with deep convolutional neural networks.☆121Updated 2 months ago
- Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)☆213Updated 2 weeks ago
- A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.☆181Updated last month
- A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.☆87Updated 5 years ago
- Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data☆115Updated 2 years ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆69Updated 7 months ago
- Benchmarking computational single cell ATAC-seq methods☆180Updated 4 years ago
- ☆91Updated 4 years ago
- TCR and BCR assembly from RNA-seq data☆294Updated this week
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆239Updated 2 months ago
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆99Updated last month
- Scanpy Tutorials.☆199Updated last week
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆67Updated last week
- ☆26Updated 3 weeks ago
- Episcanpy: Epigenomics Single Cell Analysis in Python☆142Updated 2 months ago
- Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal☆208Updated 3 weeks ago
- Benchmarking analysis of data integration tools☆332Updated last month
- T/B cell receptor sequencing analysis notes☆218Updated 2 months ago
- Package for fetching metadata and downloading data from SRA/ENA/GEO☆321Updated this week
- 📚 Tools and databases for analyzing HLA and VDJ genes.☆217Updated 2 months ago
- code to run sei and obtain sei and sequence class predictions☆97Updated 2 years ago
- [REPLACED by https://github.com/antigenomics/mirpy] Post-analysis of immune repertoire sequencing data☆133Updated 8 months ago
- Application for making ENCODE Blacklists☆288Updated 3 years ago
- A scanpy extension to analyse single-cell TCR and BCR data.☆226Updated last week