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. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Rna-seq pipeline, From FASTQ to differential expression analysis...☆20Mar 13, 2017Updated 9 years ago
- R package for bcbio single-cell RNA-seq analysis.☆31Sep 9, 2024Updated last year
- a python package for KEGG pathway enrichment analysis with multiple gene lists.☆38Nov 8, 2017Updated 8 years ago
- Training and using TFFM/PSSM/4-bits + DNA shape classifiers☆13Jun 11, 2018Updated 8 years ago
- Predicting oncogenic potential of gene fusions☆13Feb 13, 2016Updated 10 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Adaptive Daisy Model to discriminate core-fitness/context-specific essential genes in large scale CRISPR-Cas9 screens☆24Mar 29, 2019Updated 7 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
- Unsupervised correction of gene independent cell responses to CRISPR-cas9☆55Apr 28, 2023Updated 3 years ago
- A python package for the identification of lncRNA from the assembled novel transcripts☆17Oct 28, 2021Updated 4 years ago
- A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data☆16Jun 17, 2020Updated 5 years ago
- The R Bioconductor package for scMAGeCK.☆13May 25, 2026Updated 2 weeks ago
- This is code for running Orthofinder -> PAML☆13Jul 27, 2016Updated 9 years ago
- Clustering cells from single cell RNA seq assays☆46Nov 19, 2018Updated 7 years ago
- TFFM framework☆13Sep 22, 2025Updated 8 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Visualize cancer genomes with FAIR single-cell RNA-seq data☆13Jan 5, 2023Updated 3 years ago
- Manipulate genomic features and validate the syntax and reference sequence of your GFF3 files☆10Dec 26, 2022Updated 3 years ago
- An Easy to Use Analysis System for All Human Public bulk RNAseq Data!☆19Dec 8, 2022Updated 3 years ago
- Parallel implementation of OrthoMCL☆21Aug 26, 2022Updated 3 years ago
- Use cases for anndata.☆14May 20, 2026Updated 3 weeks ago
- Interactive Differential Expression AnaLysis - DE made accessible and reproducible☆33Dec 1, 2025Updated 6 months ago
- R package for DER Finder, a method for differential expression analysis of RNA-seq data☆22Mar 6, 2015Updated 11 years ago
- ☆18Oct 13, 2023Updated 2 years ago
- Normalization for single cell RNA-seq data☆51Jun 11, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- TreeExp 2.0: Toolbox for analyzing expression evolution based on RNA-seq count data☆15Jul 12, 2019Updated 6 years ago
- RNA-seq Viewer Team at the NCBI-assisted Boston Genomics Hackathon☆38Jul 24, 2017Updated 8 years ago
- A whole-genome and alignment-free prokaryotic phylogeny tool☆23May 26, 2026Updated 2 weeks ago
- Quick Read Quality Control☆20Feb 28, 2023Updated 3 years ago
- GTEx analysis scripts☆20Mar 14, 2017Updated 9 years ago
- Murine version of MCP-counter, a tool to estimate the immune and stromal composition of heterogeneous tissue, from transcriptomic data☆12Jun 30, 2022Updated 3 years ago
- Easily draw publication-quality figures of splicing quantitative trait loci☆16Feb 2, 2018Updated 8 years ago
- Analysing Capture Seq Count Data☆13Jun 11, 2018Updated 8 years ago
- ☆14Sep 11, 2023Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data☆67Apr 10, 2020Updated 6 years ago
- ChIP-seq DC and QC Pipeline☆36Mar 19, 2021Updated 5 years ago
- inference of transcription factor activity at the single cell level☆28May 27, 2026Updated 2 weeks ago
- Fast fusion detection using kallisto☆80Jun 11, 2025Updated last year
- Base-pair resolution detection of transcription factor binding site by deep deconvolutional network☆10Sep 12, 2017Updated 8 years ago
- An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter☆14Jan 18, 2019Updated 7 years ago
- A tool for evaluating RNA seq mapping☆22Jul 12, 2019Updated 6 years ago