RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).
☆56Nov 27, 2012Updated 13 years ago
Alternatives and similar repositories for rna-seq-diff-exprn
Users that are interested in rna-seq-diff-exprn are comparing it to the libraries listed below
Sorting:
- Rna-seq pipeline, From FASTQ to differential expression analysis...☆20Mar 13, 2017Updated 8 years ago
- Training and using TFFM/PSSM/4-bits + DNA shape classifiers☆13Jun 11, 2018Updated 7 years ago
- inference of transcription factor activity at the single cell level☆24Dec 16, 2025Updated 2 months ago
- A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data☆16Jun 17, 2020Updated 5 years ago
- A python package for the identification of lncRNA from the assembled novel transcripts☆17Oct 28, 2021Updated 4 years ago
- a python package for KEGG pathway enrichment analysis with multiple gene lists.☆38Nov 8, 2017Updated 8 years ago
- Classification of Single cells by Transfer Learning☆10Oct 11, 2025Updated 4 months ago
- An Easy to Use Analysis System for All Human Public bulk RNAseq Data!☆18Dec 8, 2022Updated 3 years ago
- RNA-seq Viewer Team at the NCBI-assisted Boston Genomics Hackathon☆37Jul 24, 2017Updated 8 years ago
- Parallel implementation of OrthoMCL☆21Aug 26, 2022Updated 3 years ago
- A whole-genome and alignment-free prokaryotic phylogeny tool☆23Mar 9, 2025Updated 11 months ago
- Examples analyses using the single-cell RNA-seq data from mouse cell atlases☆22Sep 16, 2019Updated 6 years ago
- Web application for clinical pharmacogenomic interpretation☆10Mar 3, 2017Updated 8 years ago
- The code for Daugherty, et al 2017 - Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans☆11Aug 24, 2017Updated 8 years ago
- A varitation graph tool☆10Dec 23, 2019Updated 6 years ago
- Quick Read Quality Control☆20Feb 28, 2023Updated 3 years ago
- Namespace encoding hierarchical relationships between proteins, protein families, and protein complexes.☆12Mar 9, 2021Updated 4 years ago
- renders a KEGGML file and displays a KEGG pathway☆10Jul 14, 2016Updated 9 years ago
- This is code for running Orthofinder -> PAML☆12Jul 27, 2016Updated 9 years ago
- ☆11Aug 6, 2019Updated 6 years ago
- A tool for evaluating RNA seq mapping☆22Jul 12, 2019Updated 6 years ago
- Adaptive Daisy Model to discriminate core-fitness/context-specific essential genes in large scale CRISPR-Cas9 screens☆24Mar 29, 2019Updated 6 years ago
- ATAC-seq lab for BIOINF545☆24Feb 17, 2026Updated last week
- ☆11Dec 15, 2025Updated 2 months ago
- Shiny app for visualization, exploration of mouse brain single cell gene expression☆11Oct 31, 2018Updated 7 years ago
- Base-pair resolution detection of transcription factor binding site by deep deconvolutional network☆10Sep 12, 2017Updated 8 years ago
- Predicting oncogenic potential of gene fusions☆12Feb 13, 2016Updated 10 years ago
- Visualize cancer genomes with FAIR single-cell RNA-seq data☆12Jan 5, 2023Updated 3 years ago
- Search public databases for given genotypic information☆11Mar 21, 2018Updated 7 years ago
- Adapted from the GATK best practice guide to preprocess whole exome sequencing (WES) data☆11Sep 4, 2019Updated 6 years ago
- single cell and bulk RNASeq analysis scripts☆14Jan 13, 2022Updated 4 years ago
- Manipulate genomic features and validate the syntax and reference sequence of your GFF3 files☆10Dec 26, 2022Updated 3 years ago
- An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter☆14Jan 18, 2019Updated 7 years ago
- ☆18Oct 13, 2023Updated 2 years ago
- TFFM framework☆13Sep 22, 2025Updated 5 months ago
- Genomic Visualization Catalog☆13Oct 6, 2022Updated 3 years ago
- Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data☆67Apr 10, 2020Updated 5 years ago
- Interactive Differential Expression AnaLysis - DE made accessible and reproducible☆31Dec 1, 2025Updated 3 months ago
- Simple tool to verticalize text delimited files.☆37May 6, 2024Updated last year