A tool to obtain and search data from the Recount2 Project at https://jhubiostatistics.shinyapps.io/recount/. The data consists of the gene, exon or exon-exon junctions, raw counts, the phenotype metadata, the URLs to the sample, or the mean coverage bigWig files.
RNA-seq
Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT "Reproducible RNA-seq analysis using recount2." Nat Biotechnol. 2017 Apr 11;35(4):319-321. https://doi.org/10.1038/nbt.3838
PMID: 28398307
PMCID: PMC6742427
Madugundu AK, Na CH, Nirujogi RS, Renuse S, Kim KP, Burns KH, Wilks C, Langmead B, Ellis SE, Collado-Torres L, Halushka MK, Kim MS, Pandey A "Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells." Proteomics. 2019 Aug;19(15):e1800315. https://doi.org/10.1002/pmic.201800315
PMID: 30983154
PMCID: PMC6812510
Ellis SE, Collado-Torres L, Jaffe A, Leek JT "Improving the value of public RNA-seq expression data by phenotype prediction." Nucleic Acids Res. 2018 May 18;46(9):e54. https://doi.org/10.1093/nar/gky102
PMID: 29514223
PMCID: PMC5961118
Jack M. Fu, Kai Kammers, Abhinav Nellore, Leonardo Collado-Torres, Jeffrey T. Leek, Margaret A. Taub "RNA-seq transcript quantification from reduced-representation data in recount2" biorxiv.org https://doi.org/10.1101/247346
Ashkaun Razmara, Shannon E. Ellis, Dustin J. Sokolowski, Sean Davis, Michael D. Wilson, Jeffrey T. Leek, Andrew E. Jaffe, Leonardo Collado-Torres "recount-brain: a curated repository of human brain RNA-seq datasets metadata" biorxiv.org https://doi.org/10.1101/618025
Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA III, Karbhari N, Hansen KD, Langmead B, Leek JT "Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive" Genome Biol. 2016 Dec 30;17(1):266. https://doi.org/10.1186/s13059-016-1118-6
PMID: 28038678
PMCID: PMC5203714
Collado-Torres L, Nellore A, Jaffe AE "recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor." F1000Res. 2017 Aug 24;6:1558. https://doi.org/10.12688/f1000research.12223.1
PMID: 29043067
PMCID: PMC5621122
Kuri-Magaña H, Collado-Torres L, Jaffe AE, Valdovinos-Torres H, Ovilla-Muñoz M, Téllez-Sosa J, Bonifaz LC, Martínez-Barnetche J "Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses." Front Immunol. 2018 Nov 21;9:2679. https://doi.org/10.3389/fimmu.2018.02679
PMID: 30519242
PMCID: PMC6260145
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600
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