CellNetCellNet: network biology applied to stem cell engineering
MINTIEMethod for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.
CellOCellO: Gene expression-based hierarchical cell type classification using the Cell Ontology
velodynDynamical systems methods for RNA velocity analysis
picardmetrics🚦 Run Picard on BAM files and collate 90 metrics into one file.
cellSNPPileup biallelic SNPs from single-cell and bulk RNA-seq data
CoNekTCoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.
gene-oracleFeature extraction algorithm for genomic data
alevin-fry🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
MetaOmGraphMetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets
tailseekerSoftware for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer
pyrpipeReproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
slamdunkStreamlining SLAM-seq analysis with ultra-high sensitivity
idealInteractive Differential Expression AnaLysis - DE made accessible and reproducible
FEELncFEELnc : FlExible Extraction of LncRNA
CICEROCICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
diffexprPorting DESeq2 and DEXSeq into python via rpy2
CD4-csawReproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
squidSQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
rnafusionRNA-seq analysis pipeline for detection gene-fusions
iDEADifferential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
NGI-RNAseqNextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
IsoQuantReference-based transcript discovery from long RNA read
READemptionA pipeline for the computational evaluation of RNA-Seq data
RATTLEReference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
biojupiesAutomated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
snakefiles🐍 Snakefiles for common RNA-seq data analysis workflows.
TransPiTransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
dee2Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
GGR-cwlCWL tools and workflows for GGR
pychopperA tool to identify, orient, trim and rescue full length cDNA reads
scCATCHAutomatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
dropPipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
Whippet.jlLightweight and Fast; RNA-seq quantification at the event-level
GREINGREIN : GEO RNA-seq Experiments Interactive Navigator
kallistobustoolskallisto | bustools workflow for pre-processing single-cell RNA-seq data
PECAPECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
haystack bioHaystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
scTCRseqProcessing of single cell RNAseq data for the recovery of TCRs in python
DGCADifferential Gene Correlation Analysis
rnatoyA proof of concept RNA-Seq pipeline with Nextflow
dolphinnextA graphical user interface for distributed data processing of high throughput genomics
DEGreportCreate a cromphensive report of DEG list coming from any analysis of RNAseq data
arribaFast and accurate gene fusion detection from RNA-Seq data
rna-seq-kallisto-sleuthA Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
kanaSingle cell analysis in the browser
grape-nfAn automated RNA-seq pipeline using Nextflow
TCC-GUI📊 Graphical User Interface for TCC package
scadenDeep Learning based cell composition analysis with Scaden.
ngs-in-biocA course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor
poreplexA versatile sequenced read processor for nanopore direct RNA sequencing
ORNAFast in-silico normalization algorithm for NGS data
NGSNext-Gen Sequencing tools from the Horvath Lab