kundajelab / bpnet
Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
☆151Updated 7 months ago
Alternatives and similar repositories for bpnet:
Users that are interested in bpnet are comparing it to the libraries listed below
- predicting expression effects of human genome variants ab initio from sequence☆127Updated last month
- TF MOtif Discovery from Importance SCOres☆134Updated last year
- Biological sequence analysis for the modern age.☆210Updated this week
- Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)☆146Updated last month
- deep learning-inspired explainable sequence model for transcription initiation☆93Updated 2 weeks ago
- Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)☆216Updated this week
- RNA-seq prediction with deep convolutional neural networks.☆133Updated this week
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆72Updated 8 months ago
- code to run sei and obtain sei and sequence class predictions☆99Updated 2 years ago
- A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.☆87Updated 5 years ago
- A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.☆183Updated 2 months ago
- 📚 Tools and databases for analyzing HLA and VDJ genes.☆219Updated 3 months ago
- A python extension for quick access to bigWig and bigBed files☆226Updated 2 months ago
- Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.☆82Updated 3 years ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆68Updated 3 weeks ago
- gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.☆251Updated this week
- Benchmarking computational single cell ATAC-seq methods☆182Updated 4 years ago
- R package to access DoRothEA's regulons☆142Updated last year
- ☆90Updated 4 years ago
- Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data☆118Updated 2 years ago
- ☆27Updated last month
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆98Updated 2 months ago
- Porting DESeq2 into python via rpy2☆68Updated last year
- Computational Optimization of DNA Activity (CODA)☆56Updated 2 months ago
- muon is a multimodal omics Python framework☆230Updated 3 weeks ago
- T/B cell receptor sequencing analysis notes☆245Updated 3 months ago
- GeneWalk identifies relevant gene functions for a biological context using network representation learning☆130Updated 7 months ago
- kallisto | bustools workflow for pre-processing single-cell RNA-seq data☆117Updated 2 years ago
- Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal☆209Updated last month
- TCR and BCR assembly from RNA-seq data☆298Updated last week