recount2

Last updated on Tue, May 9, 2023
#recount2 recount2 website Bioconductor
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In 2015 we re-processed all the human RNA-seq that was publicly available at the time in an effort to improve the usability of this complex type of data and to facilitate developing new bioinformatic and biostatistical methods. Via recount2 we have democratized the access to this rich data and this project has lead to many different publications by the recount2 team and other researchers.

recount2 bulk
Leonardo Collado-Torres
Leonardo Collado-Torres
Investigator @ LIBD, Assistant Professor, Department of Biostatistics @ JHBSPH

#rstats @Bioconductor/🧠 genomics @LieberInstitute/@lcgunam @jhubiostat @jtleek @andrewejaffe alumni/@LIBDrstats @CDSBMexico co-founder

Publications

Detection of pathogenic splicing events from RNA-sequencing data using dasper
Although next-generation sequencing technologies have accelerated the discovery of novel gene-to-disease associations, many patients …
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Detection of pathogenic splicing events from RNA-sequencing data using dasper
Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information
Genome-wide association studies have generated an increasing number of common genetic variants associated with neurological and …
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Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information
Recounting the FANTOM CAGE–Associated Transcriptome
Long noncoding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression …
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Recounting the FANTOM CAGE–Associated Transcriptome
recount-brain: a curated repository of human brain RNA-seq datasets metadata
Poster presented at BoG2019
PDF Code Project
recount-brain: a curated repository of human brain RNA-seq datasets metadata
recount-brain: a curated repository of human brain RNA-seq datasets metadata
The usability of publicly-available gene expression data is often limited by the availability of high-quality, standardized biological …
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recount-brain: a curated repository of human brain RNA-seq datasets metadata
Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses
Background: Antibody class switch recombination (CSR) to IgG, IgA or IgE is a hallmark of adaptive immunity, allowing antibody function …
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Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses
Improving the value of public RNA-seq expression data by phenotype prediction
Background: Publicly available genomic data are a valuable resource for studying normal human variation and disease, but these data are …
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Improving the value of public RNA-seq expression data by phenotype prediction
RNA-seq transcript quantification from reduced-representation data in recount2
More than 70,000 short-read RNA-sequencing samples are publicly available through the recount2 project, a curated database of summary …
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RNA-seq transcript quantification from reduced-representation data in recount2
Getting started with recount2 and accessing it via R
Poster presented at IDIES2017
PDF Project
Getting started with recount2 and accessing it via R
recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations]
The recount2 resource is composed of over 70,000 uniformly processed human RNA-seq samples spanning TCGA and SRA, including GTEx. The …
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recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations]
Reproducible RNA-seq analysis using recount2
recount2 is a resource of processed and summarized expression data spanning over 70,000 human RNA-seq samples from the Sequence Read …
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Reproducible RNA-seq analysis using recount2
Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
We found 56,861 junctions (18.6%) in at least 1000 samples that were not annotated out of 21,504 samples, and their expression associated with tissue type. We compiled junction data into a resource called intropolis available at http://intropolis.rail.bio.
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Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
Rail-RNA: Scalable analysis of RNA-seq splicing and coverage
We describe Rail-RNA, a cloud-enabled spliced aligner that analyzes many samples at once. Rail-RNA eliminates redundant work across samples, making it more efficient as samples are added. For many samples, Rail-RNA is more accurate than annotation-assisted aligners.
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Rail-RNA: Scalable analysis of RNA-seq splicing and coverage