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0
votes
2
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336
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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451
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Pan-organism OrgDb database, Accession number translated to organism name in R
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updated 5 months ago by 65k • written 5 months ago by • 0
2
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5
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765
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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
666
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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
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updated 16 months ago by ▴ 20 • written 6.4 years ago by • 0
0
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625
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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
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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
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written 9.4 years ago by ▴ 20
1
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1
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1.5k
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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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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
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1.1k
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How to convert codominant Microsatellite two column data into illumina AB format?
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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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1
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3.1k
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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
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Converting .gpr files to .csv files
Microarray GO convert
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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6
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converting probeset id to gene id's : fRMA
probe affy convert frma probe affy convert frma
updated 9.9 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?)
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updated 10.0 years ago by 65k • written 10.0 years ago by ★ 1.1k
0
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viewApply drops feature names; transfer names between lists
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Pathview question
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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
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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
votes
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
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10.1 years ago Matthias Arnold ▴ 10
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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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
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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
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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
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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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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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