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iRAP - an integrated RNA-seq Analysis Pipeline

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1038/nature08903openalex-snapshot

Transcriptome genetics using second generation sequencing in a Caucasian population

inferredcites →https://doi.org/10.1038/nbt.1621openalex-snapshot

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

inferredcites →https://doi.org/10.1038/nbt.2450openalex-snapshot

Differential analysis of gene regulation at transcript resolution with RNA-seq

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.2221openalex-snapshot

The GEM mapper: fast, accurate and versatile alignment by filtration

inferredcites →https://doi.org/10.1038/nprot.2012.016openalex-snapshot

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

inferredcites →https://doi.org/10.1093/bioinformatics/btp120openalex-snapshot

TopHat: discovering splice junctions with RNA-Seq

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot

edgeR : a Bioconductor package for differential expression analysis of digital gene expression data

inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot

Fast and accurate long-read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btq057openalex-snapshot

Fast and SNP-tolerant detection of complex variants and splicing in short reads

inferredcites →https://doi.org/10.1093/bioinformatics/btr012openalex-snapshot

A pipeline for RNA-seq data processing and quality assessment

inferredcites →https://doi.org/10.1093/bioinformatics/btr441openalex-snapshot

RseqFlow: workflows for RNA-Seq data analysis

inferredcites →https://doi.org/10.1093/bioinformatics/bts294openalex-snapshot

OSA: a fast and accurate alignment tool for RNA-Seq

inferredcites →https://doi.org/10.1093/bioinformatics/bts605openalex-snapshot

Tools for mapping high-throughput sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot

STAR: ultrafast universal RNA-seq aligner

inferredcites →https://doi.org/10.1093/bioinformatics/btt016openalex-snapshot

Grape RNA-Seq analysis pipeline environment

inferredcites →https://doi.org/10.1093/bioinformatics/btu169openalex-snapshot

PRADA: pipeline for RNA sequencing data analysis

inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot

HTSeq—a Python framework to work with high-throughput sequencing data

inferredcites →https://doi.org/10.1093/nar/gkt111openalex-snapshot

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

inferredcites →https://doi.org/10.1186/1471-2105-14-220openalex-snapshot

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

inferredcites →https://doi.org/10.1186/gb-2010-11-10-r106openalex-snapshot

Differential expression analysis for sequence count data

inferredcites →https://doi.org/10.1186/gb-2010-11-8-r86openalex-snapshot

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

inferredcites →https://doi.org/10.1186/gb-2011-12-2-r13openalex-snapshot

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

inferredcites →https://doi.org/10.3389/fgene.2011.00046openalex-snapshot

SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/ajh.25450openalex-snapshot

Integration of transcriptional and mutational data simplifies the stratification of peripheral T‐cell lymphoma

inferred← citeshttps://doi.org/10.1002/btpr.2137openalex-snapshot

An automated RNA‐Seq analysis pipeline to identify and visualize differentially expressed genes and pathways in CHO cells

inferred← citeshttps://doi.org/10.1016/j.ebiom.2020.102659openalex-snapshot

Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic alterations

inferred← citeshttps://doi.org/10.1016/j.xcrm.2022.100705openalex-snapshot

Immuno-genomic profiling of biopsy specimens predicts neoadjuvant chemotherapy response in esophageal squamous cell carcinoma

inferred← citeshttps://doi.org/10.1021/acsomega.9b02811openalex-snapshot

Detection and Quantification of GPCR mRNA: An Assessment and Implications of Data from High-Content Methods

inferred← citeshttps://doi.org/10.1038/nbt.3209openalex-snapshot

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

inferred← citeshttps://doi.org/10.1038/s41467-018-03751-6openalex-snapshot

Massive mining of publicly available RNA-seq data from human and mouse

inferred← citeshttps://doi.org/10.1038/s41467-020-16785-6openalex-snapshot

A user guide for the online exploration and visualization of PCAWG data

inferred← citeshttps://doi.org/10.1038/s41586-020-1970-0openalex-snapshot

Genomic basis for RNA alterations in cancer

inferred← citeshttps://doi.org/10.1038/s41598-020-68407-2openalex-snapshot

Genome-wide identification and characterization of Solanum tuberosum BiP genes reveal the role of the promoter architecture in BiP gene diversity

inferred← citeshttps://doi.org/10.1038/s41598-021-04284-7openalex-snapshot

Tissue specific expression of UMAMIT amino acid transporters in wheat

inferred← citeshttps://doi.org/10.1038/srep11487openalex-snapshot

Molecular and neuronal homology between the olfactory systems of zebrafish and mouse

inferred← citeshttps://doi.org/10.1093/bib/bbv036openalex-snapshot

Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective

inferred← citeshttps://doi.org/10.1093/bioinformatics/btx143openalex-snapshot

The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data

inferred← citeshttps://doi.org/10.1093/molbev/msy056openalex-snapshot

Divergence of Noncoding Regulatory Elements Explains Gene–Phenotype Differences between Human and Mouse Orthologous Genes

inferred← citeshttps://doi.org/10.1093/nar/gkaf1238openalex-snapshot

Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration

inferred← citeshttps://doi.org/10.1101/163907openalex-snapshot

A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)

inferred← citeshttps://doi.org/10.1101/183889openalex-snapshot

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

inferred← citeshttps://doi.org/10.1101/gr.176784.114openalex-snapshot

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface

inferred← citeshttps://doi.org/10.1104/pp.15.01667openalex-snapshot

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform

inferred← citeshttps://doi.org/10.1146/annurev-biodatasci-072018-021211openalex-snapshot

Connectivity Mapping: Methods and Applications

inferred← citeshttps://doi.org/10.1158/0008-5472.can-17-1679openalex-snapshot

Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer

inferred← citeshttps://doi.org/10.1158/2767-9764.crc-23-0341openalex-snapshot

Establishment and Characterization of an Epstein-Barr Virus–positive Cell Line from a Non-keratinizing Differentiated Primary Nasopharyngeal Carcinoma

inferred← citeshttps://doi.org/10.1186/s12859-019-3219-1openalex-snapshot

uap: reproducible and robust HTS data analysis

inferred← citeshttps://doi.org/10.1186/s13059-019-1637-zopenalex-snapshot

Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects

inferred← citeshttps://doi.org/10.1371/journal.pbio.3000434openalex-snapshot

GPCRs show widespread differential mRNA expression and frequent mutation and copy number variation in solid tumors

inferred← citeshttps://doi.org/10.1371/journal.pone.0107026openalex-snapshot

RNA-Seq Gene Profiling - A Systematic Empirical Comparison

inferred← citeshttps://doi.org/10.28991/esj-2019-01178openalex-snapshot

Developing an Integrated Genomic Profile for Cancer Patients with the Use of NGS Data

inferred← citeshttps://doi.org/10.3389/fimmu.2020.01470openalex-snapshot

An RNA-seq Based Machine Learning Approach Identifies Latent Tuberculosis Patients With an Active Tuberculosis Profile

inferred← citeshttps://doi.org/10.3390/ijms20030559openalex-snapshot

GPR68: An Emerging Drug Target in Cancer

inferred← citeshttps://doi.org/10.3410/f.736984636.793568776openalex-snapshot

Faculty Opinions recommendation of GPCRs show widespread differential mRNA expression and frequent mutation and copy number variation in solid tumors.

inferred← citeshttps://doi.org/10.34626/dyj8-3285openalex-snapshot

Assessing the impact of alternative splicing in cancer

inferred← citeshttps://doi.org/10.34626/qc4z-6h19openalex-snapshot

A Computational Platform for Gene Expression Analysis

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