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0
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2
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395
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NCBI protein conversion to CDNA and NCBI gene (in R)
convert
updated 5 months ago by 66k • written 5 months ago by • 0
0
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21
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BAM files to Genomic Ranges object
Alignment convert Repitools Alignment convert Repitools
updated 6 months ago by • 0 • written 11.4 years ago by ▴ 280
1
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3
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489
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Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo OrgDb convert Organismname RStudio
updated 6 months ago by 66k • written 6 months ago by • 0
2
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5
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894
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Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
6 months ago j_denton • 0
2
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1
reply
744
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Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData DataImport oligo RNASeqData convert
updated 10 months ago by 66k • written 10 months ago by • 0
1
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4
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RNA-seq analysis using R
limma rnaseq convert R
updated 13 months ago by 50k • written 5.5 years ago by ▴ 10
0
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1
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2.8k
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voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization graph limma convert edgeR DESeq Rsubread Normalization graph limma convert
updated 17 months ago by 50k • written 12.0 years ago by ★ 6.5k
0
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2
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 12.3 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 17 months ago by ▴ 20 • written 6.5 years ago by • 0
0
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converting position from '-' strand to '+' strand
convert convert
updated 23 months ago by ▴ 10 • written 14.2 years ago by ★ 1.1k
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4
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How to combine VCF-class and data.frame with annotations
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written 11.8 years ago by ▴ 70
0
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644
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TFutils database
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3.0 years ago nicocillari • 0
2
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6
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getLDS error in scan
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updated 3.6 years ago by ★ 6.5k • written 3.6 years ago by • 0
0
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3
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convert affy CEL files to data.frame??
convert convert
updated 5.7 years ago by • 0 • written 13.3 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 7.5 years ago by ★ 2.0k • written 7.5 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 7.6 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 9.5 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
8.0 years ago arvind90.psc • 0
1
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2
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2.5k
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making ExpressionSet from RGList via NChannelSet for use with 'sva'
biobase convert sva ringo arrayqualitymetrics
updated 8.2 years ago by 50k • written 8.2 years ago by • 0
1
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2
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3.4k
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minfi, bumphunter + complex experimental design, and 3 other 450K queries
GO convert minfi bumphunter GO convert minfi bumphunter
updated 8.4 years ago by ▴ 30 • written 10.0 years ago by ★ 4.0k
1
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1
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1.7k
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Error of GDS2eSet() function
convert geoquery error GDS2eSet
updated 8.4 years ago by 66k • written 8.4 years ago by • 0
0
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3
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2.0k
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Minfi "mapToGenome" error when attempting to generate a genomicRatioSet
Cancer convert minfi Cancer convert minfi
updated 8.6 years ago by • 0 • written 10.3 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?
Microsatellite Convert recode
8.6 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 8.9 years ago by ▴ 830 • written 8.9 years ago by ▴ 10
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[ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids
Sequencing Annotation convert biomaRt ReportingTools DESeq2 Sequencing Annotation convert
updated 9.4 years ago by ▴ 370 • written 10.5 years ago by ▴ 160
5
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Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
9.7 years ago patrick.schordert ▴ 30
0
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1
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2.1k
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Converting .gpr files to .csv files
Microarray GO convert
updated 9.7 years ago by 66k • written 9.7 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 9.7 years ago by ▴ 80 • written 9.7 years ago by ▴ 50
0
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0
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ChIPpeakAnno
SNP Annotation annotate convert SNP Annotation annotate convert
9.8 years ago Julie Zhu ★ 4.3k
0
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1
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2.1k
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narrow and xstringset
convert convert
updated 9.8 years ago by ★ 6.8k • written 9.8 years ago by ▴ 680
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Biomart annotation
annotate convert annotate convert
updated 9.9 years ago by ▴ 190 • written 9.9 years ago by ▴ 40
0
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ShortReadQ and conversion of quality scores to characters
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updated 9.9 years ago by 25k • written 9.9 years ago by ▴ 310
0
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SomaticSignatures
Annotation Cancer convert Annotation Cancer convert
updated 9.9 years ago by ★ 1.3k • written 9.9 years ago by ▴ 90
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converting probeset id to gene id's : fRMA
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updated 9.9 years ago by ★ 3.0k • written 10.0 years ago by ▴ 190
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7
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Approaches to building Rle sequences from ranges
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updated 10.0 years ago by ▴ 90 • written 10.0 years ago by ▴ 40
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GRanges - coercion from dataframe
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updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 10
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GenomicAlignments and QNAME collision
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updated 10.0 years ago by ▴ 90 • written 10.0 years ago by ★ 6.8k
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error on loading ratioConvert() in minfi
convert minfi convert minfi
updated 10.0 years ago by ★ 6.5k • written 10.0 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 10.1 years ago by 66k • written 10.1 years ago by ★ 1.1k
0
votes
0
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viewApply drops feature names; transfer names between lists
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0
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Pathview question
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ReportingTools gene IDs
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updated 10.1 years ago by 66k • written 10.1 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 10.1 years ago by 25k • written 10.1 years ago by ★ 7.9k
0
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0
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BiomaRt getBM error: Unknown column
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10.2 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 10.2 years ago by 16k • written 10.2 years ago by ▴ 50
0
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CellMix package use with own data matrix
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0
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crlmm problem
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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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methyAnalysis for DMR identification
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updated 10.3 years ago by ▴ 160 • written 10.3 years ago by ★ 13k
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DMR identification: minfi speed, memory problems
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updated 10.3 years ago by 66k • written 10.3 years ago by ★ 13k
50 results • Page 1 of 1
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Comment: Deseq2 by Ram ▴ 210
Cross-posted on biostars: https://www.biostars.org/p/9596031/
Comment: SpliceWiz collateData error by giulia.nicoletto.1 • 0
Hi there, I am facing a similar error. When I try the collateData command collateData( Experiment = expr, reference_path = "./Referen…
Answer: Best way to describe DEseq2 design by SamGG ▴ 350
Hi, My own opinion. In the design `~ Batch`, ChemicalA_t1 is the intercept. So, all coefficients refer to this level as a reference. …
Answer: Deseq2 by ATpoint ★ 4.2k
Ser the vignette https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html It covers prefiltering (and everyt…
Comment: Counter-directional LFC shrinkage by Michael Love 42k
Gene 1 is hard to predict given the paucity of data for the comparison of interest. What is happening is that the relatively low dispersion…
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Answer: Deseq2
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
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