0
votes
2
replies
1.5k
views
enrichPlot error when plotting topGO results
topGO enrichplot
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
1
reply
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GenomeInfoDbData version 1.2.9
GenomeInfoDbData
updated 2.2 years ago by 4.2k • written 2.2 years ago by • 0
0
votes
5
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1.9k
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minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
2.2 years ago dorota.komar • 0
2
votes
5
replies
1.9k
views
Help with orgdb for non-model species via makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 80
2
votes
2
replies
2.2k
views
Long-read mode in featureCounts
Rsubread LongRead
2.2 years ago mmisak • 0
0
votes
1
reply
857
views
Issue with weights in voomLmFit()
limma
updated 14 months ago by 53k • written 2.2 years ago by ▴ 170
0
votes
2
replies
1.6k
views
minfi differential methylation analysis errors
minfi
2.2 years ago matthew.sinton • 0
1
vote
2
replies
1.2k
views
tximeta error with vroom
tximeta vroom
2.2 years ago Pufall, Miles A ▴ 30
2
votes
4
replies
2.4k
views
Annotation Dbi Error: unable to find an inherited method for function 'x' for signature "MaskedBSgenome"
BSgenome.Hsapiens.UCSC.hg19 AnnotationDbi
2.2 years ago Erica • 0
0
votes
1
reply
1.2k
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 2.2 years ago by • 0 • written 4.4 years ago by • 0
1
vote
11
replies
3.1k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
votes
2
replies
1.1k
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
2.2 years ago georgii.vdovin • 0
0
votes
0
replies
904
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
2.2 years ago nromerov • 0
1
vote
3
replies
924
views
edgeR: Time course RNA-seq experiments
edgeR
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
3
votes
5
replies
1.7k
views
DESeq2: Design model includes sex but only one female
DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
votes
3
replies
1.5k
views
Installing Gpart
gpart heat heatmaps
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
2
votes
1
reply
1.5k
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor biocon limma
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
1
vote
7
replies
1.9k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 2.1 years ago by 53k • written 2.2 years ago by • 0
2
votes
2
replies
900
views
SeqSQC R library, functions PCA and IBD not working
SeqSQC
2.2 years ago ttom ▴ 10
0
votes
1
reply
1.7k
views
DeSeq2 normalization 16S
DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
5
votes
3
replies
1.3k
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 2.2 years ago by 53k • written 2.2 years ago by ▴ 180
0
votes
4
replies
1.5k
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
2.3 years ago • updated 2.2 years ago ar14g12 • 0
0
votes
2
replies
886
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
0
votes
1
reply
1.1k
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 2.2 years ago by • 0
0
votes
0
replies
591
views
loadstudy and cBioDataPack return error in vroom_
cBioPortalData
2.2 years ago karam • 0
0
votes
1
reply
942
views
DeSeq2 data comparison and extracting outputs
DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.3 years ago by • 0
0
votes
1
reply
1.4k
views
EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
0
replies
984
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
2
votes
4
replies
2.0k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 2.2 years ago by ▴ 10 • written 2.3 years ago by • 0
2
votes
2
replies
933
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
2.3 years ago • updated 2.2 years ago r.murakami • 0
0
votes
3
replies
1.5k
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 2.3 years ago by ▴ 780 • written 2.3 years ago by • 0
0
votes
2
replies
1.5k
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
2.3 years ago Momo • 0
0
votes
5
replies
1.6k
views
pathway finding software
written 17.2 years ago by ▴ 250
0
votes
1
reply
747
views
how to extract specific gene coordinates by passing a list of genes using homo.sapiens library
missRows
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
10
votes
11
replies
3.7k
views
tximport error: vroom
tximport
updated 2.2 years ago by • 0 • written 2.3 years ago by ▴ 40
0
votes
1
reply
848
views
Gene names from Matrix
BioCor StarBioTrek MatrixGenerics
updated 21 months ago by ▴ 760 • written 2.3 years ago by • 0
2
votes
11
replies
2.1k
views
Error MakeOrgPackagefromNCBI
Bioconductor
updated 23 months ago by ★ 4.1k • written 2.3 years ago by • 0
0
votes
5
replies
3.0k
views
Gviz: UcscTrack and "GC Percent" information
Gviz coMET
3.1 years ago • updated 2.3 years ago Daniel E. Weeks ▴ 30
1
vote
4
replies
6.2k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 3.1 years ago by • 0
1
vote
5
replies
1.6k
views
Mixed up sample info with plotPCA
plotMA ggplot2 plotPCA DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
2
votes
6
replies
1.6k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 2.3 years ago by 16k • written 2.3 years ago by • 0
0
votes
4
replies
1.1k
views
Extract LRT results for each comparison
LRT DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
2
replies
992
views
bug in block.plsda from mixOmics?
mixOmics
2.3 years ago Lluís Revilla Sancho ▴ 760
0
votes
1
reply
758
views
Is SeqSQC compatible with hg38?
SeqSQC hg38
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
2
replies
2.4k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
2.3 years ago Gregory • 0
0
votes
1
reply
1.1k
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 2.3 years ago by ▴ 780 • written 2.3 years ago by • 0
1
vote
1
reply
1.3k
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
1
vote
4
replies
1.5k
views
biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
2.3 years ago andrew.b.kleist ▴ 10
5
votes
2
replies
2.9k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
2.3 years ago Federico ▴ 10
0
votes
1
reply
722
views
error running exp2grn
NewWave
updated 2.3 years ago by ▴ 40 • written 2.4 years ago by • 0
46,705 results • Page 41 of 935
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Comment: Converting Probe IDs to HGNC symbols by Manav ▴ 10
ah thank u so much
Comment: Guitar R package requires update due to dependency GenomicFeatures by Sean Davis 21k
A great way to communicate such a nice troubleshooting and bug fix hint is to file an issue in github: https://github.com/lzcyzm/Guitar/iss…
Answer: Converting Probe IDs to HGNC symbols by Sean Davis 21k
The brainarray annotations are very confusing, as the IDs in the fData look like affymetrix probe IDs. To clarify, the brainarray project m…
Comment: How to do differential expresion across time serise with edgeR? by Gordon Smyth 53k
If you have fake replicates, then I think my code answers your question about how to run the edgeR time-course analysis. Regarding tutoria…
Comment: How to do differential expresion across time serise with edgeR? by petergrahamclark ▴ 10
The use case is kinetic model parameterisation. I'm actually a systems biologist not a bioinformatician. (which is why I'm struggling here)…
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Answer: Converting Probe IDs to HGNC symbols
Converting Probe IDs to HGNC symbols
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