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Search results for pipeline rna seq

64 search results found

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

Sequana ⭐ 136

Sequana: a set of Snakemake NGS pipelines

Rnaseq Workflow ⭐ 133

A repository for setting up a RNAseq workflow

Seq2science ⭐ 132

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Rnafusion ⭐ 120

RNA-seq analysis pipeline for detection gene-fusions

Scrnaseq ⭐ 119

A single-cell RNAseq pipeline for 10X genomics data

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

Rnalysis ⭐ 114

RNA sequencing analysis software

Pipeline Transcriptome De ⭐ 95

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

Biojupies ⭐ 94

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

Dolphinnext ⭐ 92

A graphical user interface for distributed data processing of high throughput genomics

Callings Nf ⭐ 76

GATK RNA-Seq Variant Calling in Nextflow

Zika Rnaseq Pipeline ⭐ 73

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

Long Reads Annotation pipeline

Rnaseq Nf ⭐ 59

A proof of concept of RNAseq pipeline

integrated RNA-seq Analysis Pipeline

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions

Tomicsvis ⭐ 50

Transcriptomics Visualization R package.

Ngi Rnaseq ⭐ 49

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

Pipeliner ⭐ 44

An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.

Metasra Pipeline ⭐ 42

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Grape Nf ⭐ 35

An automated RNA-seq pipeline using Nextflow

Pipeline Nanopore Ref Isoforms ⭐ 35

Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools

Spatialtranscriptomics ⭐ 34

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Differentialabundance ⭐ 34

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

Ngs_pipeline ⭐ 31

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Rnadeseq ⭐ 31

Differential gene expression analysis and pathway analysis of RNAseq data

Reademption ⭐ 31

A pipeline for the computational evaluation of RNA-Seq data

RNASeq pipeline

Pipeliner ⭐ 25

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

A proof of concept RNA-Seq pipeline with Nextflow

ASAP : Automated Single-cell Analysis Pipeline

gatk4 RNA variant calling pipeline

Pipeline Pinfish Analysis ⭐ 22

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Rnaseq Nf ⭐ 20

RNAseq analysis pipeline

Rna Seq Snakemake ⭐ 20

Snakemake based pipeline for RNA-Seq analysis

Master of Pores 2

Pigx_rnaseq ⭐ 19

Pipeline for RNAseq

Pipeline Nanopore Denovo Isoforms ⭐ 19

Pipeline for de novo clustering of long transcriptomic reads

Rnasplice ⭐ 18

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

Tailseeker ⭐ 18

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

Rnaseq Pipeline ⭐ 18

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample

Open_pipelines ⭐ 17

Pipelines for NGS data preprocessing by the Bock lab and friends

Pipernaseq ⭐ 16

A comprehensive pipeline for RNAseq data analysis

parseR: Pipeline for rna-seq analysis in R

Pipelines in genomics

Flexible omics pipeline

RNA-seq, QC and differential analysis pipeline

Seq Pipeline ⭐ 12

Workspace for data science projects and NGS pipelines. Contains RStudio, Jupyter Notebook, VSCode and file manager. Can connect to Tailscale network to bypass firewalls.

Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.

Xpresspipe ⭐ 11

An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data

Enrichment_analysis ⭐ 10

A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.

Tostadas ⭐ 10

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Piperiboseq ⭐ 10

A comprehensive pipeline for Ribo-seq data analysis

Rnaseq Pipeline ⭐ 9

RNASeq-Pipeline for Quantification and Enrichment Analysis

A comprehensive quality-control and quantification RNA-seq pipeline

Bgee_pipeline ⭐ 8

Source code of the Bgee pipeline used to build the Bgee database

Nextgenseq_pipeline ⭐ 8

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Dualrnaseq ⭐ 7

Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

Extensible full DAG streaming computation server with services and jobs for RNA-Seq, Tn-Seq, WG-Seq and Term-Seq.

Braincode ⭐ 7

Script and pipeline for BRAINcode project

Plants Pipeline ⭐ 6

This project is an automated pipeline to generate annotated gene expression atlases for kingdoms of life

Speaqeasy ⭐ 6

SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.

Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments

Rnaseq_workflow ⭐ 6

snakemake workflow for bulk RNA-seq workflow using STAR-edgeR

KnowSeq R package

3’ Tag RNA-seq pipeline (Work in progress)

Bioinformatics_pipeline ⭐ 5

Bioinformatics Pipeline

Ribo Oddr ⭐ 5

Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs

As_analysis ⭐ 5

A complete Snakemake pipeline for detecting allele specific expression

Automated and friendly RNA-seq analysis (deprecated)

Ribomethseq Nf ⭐ 5

Nextflow pipeline dedicated to RiboMethSeq data processing

Epitope discovery pipeline for RNA-seq

Integrative Pipeline for Splicing Analyses (IPSA) in Nextflow

Genome_tracks ⭐ 5

A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files powered by the wrapper gtracks for the package pyGenomeTracks.

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