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Top 60 rna-seq open source projects

CellNet
CellNet: network biology applied to stem cell engineering
MINTIE
Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.
velodyn
Dynamical systems methods for RNA velocity analysis
picardmetrics
🚦 Run Picard on BAM files and collate 90 metrics into one file.
cellSNP
Pileup biallelic SNPs from single-cell and bulk RNA-seq data
CoNekT
CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.
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.
MetaOmGraph
MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets
tailseeker
Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer
pyrpipe
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
ideal
Interactive Differential Expression AnaLysis - DE made accessible and reproducible
FEELnc
FEELnc : FlExible Extraction of LncRNA
CICERO
CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
diffexpr
Porting DESeq2 and DEXSeq into python via rpy2
CD4-csaw
Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
squid
SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
iDEA
Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
cruk-summer-school-2018
Summer school course materials collection
NGI-RNAseq
Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
IsoQuant
Reference-based transcript discovery from long RNA read
READemption
A pipeline for the computational evaluation of RNA-Seq data
RATTLE
Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
biojupies
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
OrchestratingSingleCellAnalysis-release
An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.
snakefiles
🐍 Snakefiles for common RNA-seq data analysis workflows.
TransPi
TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
dee2
Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
pychopper
A tool to identify, orient, trim and rescue full length cDNA reads
scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
drop
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
Whippet.jl
Lightweight and Fast; RNA-seq quantification at the event-level
kallistobustools
kallisto | bustools workflow for pre-processing single-cell RNA-seq data
PECA
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
pipeline-pinfish-analysis
Pipeline for annotating genomes using long read transcriptomics data with pinfish
scTCRseq
Processing of single cell RNAseq data for the recovery of TCRs in python
DGCA
Differential Gene Correlation Analysis
rnatoy
A proof of concept RNA-Seq pipeline with Nextflow
DEGreport
Create a cromphensive report of DEG list coming from any analysis of RNAseq data
Subread to DEXSeq
Scripts to import your FeatureCounts output into DEXSeq
rna-seq-kallisto-sleuth
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
grape-nf
An automated RNA-seq pipeline using Nextflow
TCC-GUI
📊 Graphical User Interface for TCC package
Protocols-4pub
Multi-omics analysis protocols by Lyu.
ngs-in-bioc
A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor
poreplex
A versatile sequenced read processor for nanopore direct RNA sequencing
NGS
Next-Gen Sequencing tools from the Horvath Lab
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