Bioconductor (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Bioconductor" in English language version.

refsWebsite

Global rank English rank

28nih.gov

4^th place

15doi.org

2^nd place

6bioconductor.org

low place

1cutadapt.readthedocs.io

low place

1ggplot2-book.org

low place

1rdrr.io

low place

bioconductor.org (Global: low place; English: low place)

"Bioconductor – Release Announcements". bioconductor.org. Bioconductor. Retrieved 28 May 2019.
"Org.Hs.eg.db".
"GenomicAlignments (Development version)".
"GenomicFeatures (Development version)".
"AnnotationHub (Development version)".
"Org.Mm.eg.db".

cutadapt.readthedocs.io (Global: low place; English: low place)

"Cutadapt — Cutadapt 5.1 documentation".

doi.org (Global: 2^nd place; English: 2^nd place)

Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W (August 2005). "BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis". Bioinformatics. 21 (16): 3439–40. doi:10.1093/bioinformatics/bti525. PMID 16082012.
Love MI, Huber W, Anders S (2014). "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2". Genome Biol. 15 (12) 550. doi:10.1186/s13059-014-0550-8. PMC 4302049. PMID 25516281.
Robinson MD, McCarthy DJ, Smyth GK (January 2010). "edgeR: a Bioconductor package for differential expression analysis of digital gene expression data". Bioinformatics. 26 (1): 139–40. doi:10.1093/bioinformatics/btp616. PMC 2796818. PMID 19910308.
Law CW, Alhamdoosh M, Su S, Dong X, Tian L, Smyth GK, Ritchie ME (2016). "RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR". F1000Res. 5 ISCB Comm J-1408. doi:10.12688/f1000research.9005.3. PMC 4937821. PMID 27441086.
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (April 2015). "limma powers differential expression analyses for RNA-sequencing and microarray studies". Nucleic Acids Res. 43 (7): e47. doi:10.1093/nar/gkv007. PMC 4402510. PMID 25605792.
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 J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (February 2015). "Orchestrating high-throughput genomic analysis with Bioconductor". Nat Methods. 12 (2): 115–21. doi:10.1038/nmeth.3252. PMC 4509590. PMID 25633503.
Liao Y, Smyth GK, Shi W (May 2019). "The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads". Nucleic Acids Res. 47 (8): e47. doi:10.1093/nar/gkz114. PMC 6486549. PMID 30783653.
Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R (October 2009). "ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data". Bioinformatics. 25 (19): 2607–8. doi:10.1093/bioinformatics/btp450. PMC 2752612. PMID 19654119.
Liao Y, Smyth GK, Shi W (April 2014). "featureCounts: an efficient general purpose program for assigning sequence reads to genomic features". Bioinformatics. 30 (7): 923–30. doi:10.1093/bioinformatics/btt656. PMID 24227677.
Koch CM, Chiu SF, Akbarpour M, Bharat A, Ridge KM, Bartom ET, Winter DR (August 2018). "A Beginner's Guide to Analysis of RNA Sequencing Data". Am J Respir Cell Mol Biol. 59 (2): 145–157. doi:10.1165/rcmb.2017-0430TR. PMC 6096346. PMID 29624415.
Chen Y, Lun AT, Smyth GK (2016). "From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline". F1000Res. 5: 1438. doi:10.12688/f1000research.8987.2. PMC 4934518. PMID 27508061.
Liao Y, Smyth GK, Shi W (May 2013). "The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote". Nucleic Acids Res. 41 (10): e108. doi:10.1093/nar/gkt214. PMC 3664803. PMID 23558742.
Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM (April 2010). "The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants". Nucleic Acids Res. 38 (6): 1767–71. doi:10.1093/nar/gkp1137. PMC 2847217. PMID 20015970.
Bolger AM, Lohse M, Usadel B (August 2014). "Trimmomatic: a flexible trimmer for Illumina sequence data". Bioinformatics. 30 (15): 2114–20. doi:10.1093/bioinformatics/btu170. PMC 4103590. PMID 24695404.
Xu T, Su N, Liu L, Zhang J, Wang H, Zhang W, Gui J, Yu K, Li J, Le TD (December 2018). "miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase". BMC Bioinformatics. 19 (Suppl 19) 514. doi:10.1186/s12859-018-2531-5. PMC 6311916. PMID 30598108.

ggplot2-book.org (Global: low place; English: low place)

"1 Introduction – ggplot2: Elegant Graphics for Data Analysis (3e)".

nih.gov (Global: 4^th place; English: 4^th place)

pubmed.ncbi.nlm.nih.gov

Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W (August 2005). "BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis". Bioinformatics. 21 (16): 3439–40. doi:10.1093/bioinformatics/bti525. PMID 16082012.
Love MI, Huber W, Anders S (2014). "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2". Genome Biol. 15 (12) 550. doi:10.1186/s13059-014-0550-8. PMC 4302049. PMID 25516281.
Robinson MD, McCarthy DJ, Smyth GK (January 2010). "edgeR: a Bioconductor package for differential expression analysis of digital gene expression data". Bioinformatics. 26 (1): 139–40. doi:10.1093/bioinformatics/btp616. PMC 2796818. PMID 19910308.
Law CW, Alhamdoosh M, Su S, Dong X, Tian L, Smyth GK, Ritchie ME (2016). "RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR". F1000Res. 5 ISCB Comm J-1408. doi:10.12688/f1000research.9005.3. PMC 4937821. PMID 27441086.
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (April 2015). "limma powers differential expression analyses for RNA-sequencing and microarray studies". Nucleic Acids Res. 43 (7): e47. doi:10.1093/nar/gkv007. PMC 4402510. PMID 25605792.
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 J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (February 2015). "Orchestrating high-throughput genomic analysis with Bioconductor". Nat Methods. 12 (2): 115–21. doi:10.1038/nmeth.3252. PMC 4509590. PMID 25633503.
Liao Y, Smyth GK, Shi W (May 2019). "The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads". Nucleic Acids Res. 47 (8): e47. doi:10.1093/nar/gkz114. PMC 6486549. PMID 30783653.
Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R (October 2009). "ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data". Bioinformatics. 25 (19): 2607–8. doi:10.1093/bioinformatics/btp450. PMC 2752612. PMID 19654119.
Liao Y, Smyth GK, Shi W (April 2014). "featureCounts: an efficient general purpose program for assigning sequence reads to genomic features". Bioinformatics. 30 (7): 923–30. doi:10.1093/bioinformatics/btt656. PMID 24227677.
Koch CM, Chiu SF, Akbarpour M, Bharat A, Ridge KM, Bartom ET, Winter DR (August 2018). "A Beginner's Guide to Analysis of RNA Sequencing Data". Am J Respir Cell Mol Biol. 59 (2): 145–157. doi:10.1165/rcmb.2017-0430TR. PMC 6096346. PMID 29624415.
Chen Y, Lun AT, Smyth GK (2016). "From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline". F1000Res. 5: 1438. doi:10.12688/f1000research.8987.2. PMC 4934518. PMID 27508061.
Liao Y, Smyth GK, Shi W (May 2013). "The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote". Nucleic Acids Res. 41 (10): e108. doi:10.1093/nar/gkt214. PMC 3664803. PMID 23558742.
Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM (April 2010). "The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants". Nucleic Acids Res. 38 (6): 1767–71. doi:10.1093/nar/gkp1137. PMC 2847217. PMID 20015970.
Bolger AM, Lohse M, Usadel B (August 2014). "Trimmomatic: a flexible trimmer for Illumina sequence data". Bioinformatics. 30 (15): 2114–20. doi:10.1093/bioinformatics/btu170. PMC 4103590. PMID 24695404.
Xu T, Su N, Liu L, Zhang J, Wang H, Zhang W, Gui J, Yu K, Li J, Le TD (December 2018). "miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase". BMC Bioinformatics. 19 (Suppl 19) 514. doi:10.1186/s12859-018-2531-5. PMC 6311916. PMID 30598108.

ncbi.nlm.nih.gov

Love MI, Huber W, Anders S (2014). "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2". Genome Biol. 15 (12) 550. doi:10.1186/s13059-014-0550-8. PMC 4302049. PMID 25516281.
Robinson MD, McCarthy DJ, Smyth GK (January 2010). "edgeR: a Bioconductor package for differential expression analysis of digital gene expression data". Bioinformatics. 26 (1): 139–40. doi:10.1093/bioinformatics/btp616. PMC 2796818. PMID 19910308.
Law CW, Alhamdoosh M, Su S, Dong X, Tian L, Smyth GK, Ritchie ME (2016). "RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR". F1000Res. 5 ISCB Comm J-1408. doi:10.12688/f1000research.9005.3. PMC 4937821. PMID 27441086.
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (April 2015). "limma powers differential expression analyses for RNA-sequencing and microarray studies". Nucleic Acids Res. 43 (7): e47. doi:10.1093/nar/gkv007. PMC 4402510. PMID 25605792.
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 J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (February 2015). "Orchestrating high-throughput genomic analysis with Bioconductor". Nat Methods. 12 (2): 115–21. doi:10.1038/nmeth.3252. PMC 4509590. PMID 25633503.
Liao Y, Smyth GK, Shi W (May 2019). "The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads". Nucleic Acids Res. 47 (8): e47. doi:10.1093/nar/gkz114. PMC 6486549. PMID 30783653.
Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R (October 2009). "ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data". Bioinformatics. 25 (19): 2607–8. doi:10.1093/bioinformatics/btp450. PMC 2752612. PMID 19654119.
Koch CM, Chiu SF, Akbarpour M, Bharat A, Ridge KM, Bartom ET, Winter DR (August 2018). "A Beginner's Guide to Analysis of RNA Sequencing Data". Am J Respir Cell Mol Biol. 59 (2): 145–157. doi:10.1165/rcmb.2017-0430TR. PMC 6096346. PMID 29624415.
Chen Y, Lun AT, Smyth GK (2016). "From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline". F1000Res. 5: 1438. doi:10.12688/f1000research.8987.2. PMC 4934518. PMID 27508061.
Liao Y, Smyth GK, Shi W (May 2013). "The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote". Nucleic Acids Res. 41 (10): e108. doi:10.1093/nar/gkt214. PMC 3664803. PMID 23558742.
Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM (April 2010). "The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants". Nucleic Acids Res. 38 (6): 1767–71. doi:10.1093/nar/gkp1137. PMC 2847217. PMID 20015970.
Bolger AM, Lohse M, Usadel B (August 2014). "Trimmomatic: a flexible trimmer for Illumina sequence data". Bioinformatics. 30 (15): 2114–20. doi:10.1093/bioinformatics/btu170. PMC 4103590. PMID 24695404.
Xu T, Su N, Liu L, Zhang J, Wang H, Zhang W, Gui J, Yu K, Li J, Le TD (December 2018). "miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase". BMC Bioinformatics. 19 (Suppl 19) 514. doi:10.1186/s12859-018-2531-5. PMC 6311916. PMID 30598108.

rdrr.io (Global: low place; English: low place)

"Pheatmap: Pretty Heatmaps version 1.0.13 from CRAN".

Bioconductor (English Wikipedia)

bioconductor.org (Global: low place; English: low place)

cutadapt.readthedocs.io (Global: low place; English: low place)

doi.org (Global: 2nd place; English: 2nd place)

ggplot2-book.org (Global: low place; English: low place)

nih.gov (Global: 4th place; English: 4th place)

pubmed.ncbi.nlm.nih.gov

ncbi.nlm.nih.gov

rdrr.io (Global: low place; English: low place)

doi.org (Global: 2^nd place; English: 2^nd place)

nih.gov (Global: 4^th place; English: 4^th place)