Effector and Perturbation Estimation Engine (EPEE) conducts differential analysis of transcription factor activity from gene expression data.
☆16Oct 3, 2019Updated 6 years ago
Alternatives and similar repositories for EPEE
Users that are interested in EPEE are comparing it to the libraries listed below
Sorting:
- Pipeline to find transcription factor footprints in DNase-seq or ATAC-seq datasets☆12Nov 24, 2018Updated 7 years ago
- Homebrew/science is deprecated☆11Jan 2, 2018Updated 8 years ago
- ☆11Jan 7, 2020Updated 6 years ago
- Code for the paper "BIOLITMAP: a web-based geolocated and temporal visualization of the evolution of bioinformatics publications" in Oxfo…☆20May 3, 2019Updated 6 years ago
- Predicting TF sequence-specificity similarity with weighted alignments☆13Oct 7, 2019Updated 6 years ago
- Base-pair resolution detection of transcription factor binding site by deep deconvolutional network☆10Sep 12, 2017Updated 8 years ago
- ☆14Sep 1, 2024Updated last year
- Handy list of network visualisation libraries for R☆12Nov 11, 2019Updated 6 years ago
- RIESLING: Super-enhancer identification. (Rapid Identification of EnhancerS LInked to Nearby Genes)☆10Jun 28, 2018Updated 7 years ago
- S3norm ver2 + IDEAS epigenetic state / master peak list☆12Sep 22, 2023Updated 2 years ago
- ☆14May 26, 2020Updated 5 years ago
- A pipeline for identifying indel derived neoantigens using RNA-Seq data☆30Aug 29, 2022Updated 3 years ago
- Training and using TFFM/PSSM/4-bits + DNA shape classifiers☆13Jun 11, 2018Updated 7 years ago
- Repo that aids in the detection of microsatellite instabilities (MSI) from sequencing data☆21Apr 22, 2024Updated last year
- Identified novel mouse spermatogenesis biomarkers based on single-cell RNA sequencing data☆11Jun 7, 2022Updated 3 years ago
- Representation of Module Activity☆10May 31, 2017Updated 8 years ago
- Integration ribosome profiling - mass spectrometry☆15Nov 4, 2025Updated 4 months ago
- Code for reproducing results from the paper "Modular and efficient pre-processing of single-cell RNA-seq data"☆23Feb 14, 2021Updated 5 years ago
- Lightweight pipeline for processing droplet-based single-cell RNA-seq data☆18Nov 4, 2020Updated 5 years ago
- cross-species analysis of cell identities, markers and regulations☆12Jul 11, 2025Updated 8 months ago
- Web version of GenomeRunner☆11Nov 6, 2016Updated 9 years ago
- Resources for Drug Repurposing In Alzheimer's Disease (DRIAD) work☆11Mar 4, 2021Updated 5 years ago
- An implementation of vConv layer.☆11Apr 28, 2021Updated 4 years ago
- NaRnEA (Nonparametric analytical Rank-based Enrichment Analysis)☆11Mar 2, 2023Updated 3 years ago
- Identify cell barcodes from single-cell genomics sequencing experiments☆43Dec 14, 2021Updated 4 years ago
- BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequenc…☆31May 20, 2025Updated 10 months ago
- Repository for the clone2vec python package☆15Updated this week
- ☆12Dec 12, 2018Updated 7 years ago
- ☆41Aug 18, 2020Updated 5 years ago
- ☆10Jan 19, 2019Updated 7 years ago
- Interpretable bimodal network for transcription factors binding site prediction☆10Jun 29, 2023Updated 2 years ago
- Code for reproducing the Sei manuscript results☆17Jan 25, 2022Updated 4 years ago
- Package for pooling the results from (dependent) tests☆12Dec 1, 2025Updated 3 months ago
- tGPLVM: A Nonparametric, Generative Model for Manifold Learning with scRNA-seq experimental data☆17Jun 4, 2019Updated 6 years ago
- The Self-Assembling-Manifold (SAM) algorithm.☆46Dec 26, 2025Updated 2 months ago
- Constructing gene regulatory networks by integrating scRNA-seq and scATAC-seq data☆13Dec 7, 2021Updated 4 years ago
- ☆12Oct 23, 2023Updated 2 years ago
- R package for high-throughput DNA shape predictions and feature encoding☆20Jul 1, 2021Updated 4 years ago
- Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously☆37Mar 20, 2023Updated 3 years ago