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0
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2
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335
views
NCBI protein conversion to CDNA and NCBI gene (in R)
convert
updated 4 months ago by 65k • written 4 months ago by • 0
1
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3
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448
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Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo OrgDb convert Organismname RStudio
updated 5 months ago by 65k • written 5 months ago by • 0
2
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5
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759
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Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
5 months ago j_denton • 0
2
votes
1
reply
663
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Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
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updated 9 months ago by 65k • written 9 months ago by • 0
0
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2
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 12.2 years ago by ▴ 190
1
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2
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How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 16 months ago by ▴ 20 • written 6.4 years ago by • 0
0
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TFutils database
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2.9 years ago nicocillari • 0
2
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6
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getLDS error in scan
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updated 3.5 years ago by ★ 6.5k • written 3.5 years ago by • 0
1
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4
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RNA-seq analysis using R
limma rnaseq convert R
updated 12 months ago by 50k • written 5.4 years ago by • 0
0
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3
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convert affy CEL files to data.frame??
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updated 5.6 years ago by • 0 • written 13.2 years ago by ▴ 40
1
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7
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Can XCMS output continuum/profile data to netCDF format?
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updated 7.4 years ago by ★ 2.0k • written 7.4 years ago by • 0
1
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3
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To convert MAList to ExpressionSet using R package 'convert'
convert
updated 7.5 years ago by 50k • written 7.5 years ago by • 0
0
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5
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How to reverse translate amino acid sequence into mammalian codon optimised cDNA
convert translation
written 9.4 years ago by ▴ 20
1
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1
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1.4k
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converting amino-acid one letter code into cDNA sequene
convert aminoacid-onlettercode cDNA
7.9 years ago arvind90.psc • 0
1
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2
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making ExpressionSet from RGList via NChannelSet for use with 'sva'
biobase convert sva ringo arrayqualitymetrics
updated 8.1 years ago by 50k • written 8.1 years ago by • 0
1
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2
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3.3k
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minfi, bumphunter + complex experimental design, and 3 other 450K queries
GO convert minfi bumphunter GO convert minfi bumphunter
updated 8.3 years ago by ▴ 30 • written 9.9 years ago by ★ 3.9k
1
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1
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1.6k
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Error of GDS2eSet() function
convert geoquery error GDS2eSet
updated 8.3 years ago by 65k • written 8.3 years ago by • 0
0
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3
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Minfi "mapToGenome" error when attempting to generate a genomicRatioSet
Cancer convert minfi Cancer convert minfi
updated 8.5 years ago by • 0 • written 10.2 years ago by ★ 6.5k
0
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How to convert codominant Microsatellite two column data into illumina AB format?
Microsatellite Convert recode
8.5 years ago parka • 0
0
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3
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11k
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How to combine expression values of multiple probes for one gene
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updated 8.8 years ago by ▴ 830 • written 8.8 years ago by ▴ 10
6
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3.0k
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[ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids
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updated 9.3 years ago by ▴ 370 • written 10.4 years ago by ▴ 160
5
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2.0k
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Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
9.6 years ago patrick.schordert ▴ 30
0
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1
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2.0k
views
Converting .gpr files to .csv files
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updated 9.6 years ago by 65k • written 9.6 years ago by ★ 13k
0
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5
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Motif enrichment analysis: Error in transfac format and background frequencies from BSGenome
BSgenome convert BSgenome PWMEnrich MotifDb
updated 9.6 years ago by ▴ 80 • written 9.6 years ago by ▴ 50
0
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ChIPpeakAnno
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9.7 years ago Julie Zhu ★ 4.3k
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1
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2.0k
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narrow and xstringset
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updated 9.7 years ago by ★ 6.8k • written 9.7 years ago by ▴ 680
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Biomart annotation
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updated 9.8 years ago by ▴ 190 • written 9.8 years ago by ▴ 40
0
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ShortReadQ and conversion of quality scores to characters
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updated 9.8 years ago by 25k • written 9.8 years ago by ▴ 310
0
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SomaticSignatures
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updated 9.8 years ago by ★ 1.3k • written 9.8 years ago by ▴ 90
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converting probeset id to gene id's : fRMA
probe affy convert frma probe affy convert frma
updated 9.8 years ago by ★ 3.0k • written 9.9 years ago by ▴ 190
0
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7
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Approaches to building Rle sequences from ranges
GO convert GO convert
updated 9.9 years ago by ▴ 90 • written 9.9 years ago by ▴ 40
0
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GRanges - coercion from dataframe
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updated 9.9 years ago by ★ 11k • written 9.9 years ago by ▴ 10
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GenomicAlignments and QNAME collision
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updated 9.9 years ago by ▴ 90 • written 9.9 years ago by ★ 6.8k
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error on loading ratioConvert() in minfi
convert minfi convert minfi
updated 9.9 years ago by ★ 6.5k • written 9.9 years ago by ★ 13k
1
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2
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Mapping gene symbols to gene names (org.Hs.eg.db?)
convert convert
updated 10.0 years ago by 65k • written 10.0 years ago by ★ 1.1k
0
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0
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viewApply drops feature names; transfer names between lists
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10.0 years ago Chris Seidel ▴ 80
0
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Pathview question
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10.0 years ago Luo Weijun ★ 1.6k
0
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9
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ReportingTools gene IDs
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updated 10.0 years ago by 65k • written 10.0 years ago by ★ 1.5k
0
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5
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summarizeOverlaps using GRanges or bed file as reads?
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updated 10.0 years ago by 25k • written 10.0 years ago by ★ 7.9k
0
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0
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BiomaRt getBM error: Unknown column
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10.1 years ago Guest User ★ 13k
0
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5
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A question about the function readGAlignmentPairs in GenomicRnages package
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updated 10.1 years ago by 16k • written 10.1 years ago by ▴ 50
0
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0
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CellMix package use with own data matrix
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10.1 years ago Riba Michela ▴ 90
0
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0
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crlmm problem
SNP convert beadarray crlmm SNP convert beadarray crlmm
10.1 years ago Matthias Arnold ▴ 10
0
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0
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DMR identification: minfi speed, memory problems
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10.2 years ago Allegra Petti ▴ 120
0
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8
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2.2k
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methyAnalysis for DMR identification
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updated 10.2 years ago by ▴ 160 • written 10.2 years ago by ★ 13k
0
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6
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DMR identification: minfi speed, memory problems
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updated 10.2 years ago by 65k • written 10.2 years ago by ★ 13k
0
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Tigre Package question 3
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updated 10.2 years ago by ▴ 60 • written 10.2 years ago by ▴ 50
0
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2
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Minfi "mapToGenome" error when attempting to generate a genomicRatioSet
convert minfi convert minfi
updated 10.2 years ago by ★ 6.5k • written 10.2 years ago by ▴ 30
0
votes
1
reply
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Using GOstats with ScanArray Express Data
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updated 10.2 years ago by ★ 13k • written 10.2 years ago by ★ 13k
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ChIPpeakAnno: TSS at - strand
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50 results • Page 1 of 1
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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