A pipeline for de novo transcriptome assembly of short reads from bulk RNA-seq

Spatial Transcriptomics

Pipeline for processing 10x Genomics single cell rnaseq data

Alternative splicing analysis using RNA-seq.

Nextflow rnafusion analysis pipeline, part of the nf-core community.

Dual RNA-seq pipeline

Differential abundance analysis

ANNOTATO - Annotation workflow To Annotate Them Oll

• ANNOTATO - Annotation workflow To Annotate Them Oll
• Overview of the workflow
• Input data
• Pipeline steps
• Output data
• Prerequisites
• Installation
• Running ANNOTATO
• Before running the pipeline (IMPORTANT) ...

ZARP

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sqtlseeker2-nf

A pipeline for splicing quantitative trait loci (sQTL) mapping.

The pipeline performs the following analysis steps:

• Index the genotype file
• Preprocess the transcript expression data
• Test for association between ...

MultiAffinity enables the study of how gene dysregulation propagates on a multilayer network on a disease of interest, uncovering key genes. Find the detailed documentation for the tool here.

Flashlite-Trinity contains two workflows that run Trinity on the University of Queensland's HPC, Flashlite. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. Users can run Flashlite-Trinity on single samples, or smaller samples requiring <500Gb ...

RNASeq-DE @ NCI-Gadi processes RNA sequencing data (single, paired and/or multiplexed) for differential expression (raw FASTQ to counts). This pipeline consists of multiple stages and is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes to run each stage in parallel.

Infrastructure_deployment_metadata: Gadi (NCI)

Description: Trinity @ NCI-Gadi contains a staged Trinity workflow that can be run on the National Computational Infrastructure’s (NCI) Gadi supercomputer. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. ...

COnSensus Interaction Network InFErence Service

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.

Reference

[Manica, Matteo, Charlotte, Bunne, Roland, Mathis, Joris, Cadow, Mehmet Eren, Ahsen, Gustavo A, Stolovitzky, and María Rodríguez, Martínez. "COSIFER: a python package for the consensus inference of molecular interaction ...

COnSensus Interaction Network InFErence Service

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.

Reference

[Manica, Matteo, Charlotte, Bunne, Roland, Mathis, Joris, Cadow, Mehmet Eren, Ahsen, Gustavo A, Stolovitzky, and María Rodríguez, Martínez. "COSIFER: a python package for the consensus inference of molecular ...

Workflow for Spliced RNAseq data Steps:

• workflow_quality.cwl:
• FastQC (Read Quality Control)
• fastp (Read Trimming)
• STAR (Read mapping)
• featurecounts (transcript read counts)
• kallisto (transcript [pseudo]counts)

RNA-Seq pipeline

Here we provide the tools to perform paired end or single read RNA-Seq analysis including raw data quality control, differential expression (DE) analysis and functional annotation. As input files you may use either zipped fastq-files (.fastq.gz) or mapped read data (.bam files). In case of paired end reads, corresponding fastq files should be named using .R1.fastq.gz and .R2.fastq.gz suffixes.

Pipeline Workflow

All analysis steps are illustrated in the pipeline ...

RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.