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0
votes
0
replies
577
views
What is the significance of DMR in DMRcate
DMRcate
22 months ago
chuanjiao6
• 0
0
votes
0
replies
459
views
HiCDCPlus differential interaction error
HiCDCPlus
23 months ago
Irene
• 0
0
votes
0
replies
682
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
23 months ago
Thalita
• 0
1
vote
1
reply
960
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 21 months ago by
Yang Liao
▴ 450 • written 23 months ago by
Joe Marturano
▴ 10
0
votes
0
replies
429
views
Postdoc
TCGAWorkflow
23 months ago
sameerahmadguru
• 0
2
votes
6
replies
5.4k
views
Looking for documentation about the use of "split = .sign" in enrichplot's dotplot
enrichplot
23 months ago • updated 22 months ago
Tobias
• 0
1
vote
1
reply
996
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 23 months ago by
alan.ocallaghan
▴ 160 • written 23 months ago by
Dario Strbenac
★ 1.6k
0
votes
1
reply
690
views
Annotatr Duplicate Entries
annotatr
AnnotationHub
written 23 months ago by
hayleyw
• 0
0
votes
0
replies
461
views
IlluminaHumanMethylation27kanno.ilmn12.hg19 package is mapped to hg18 genome
IlluminaHumanMethylation27kanno.ilmn12.hg19
23 months ago
Basti
▴ 780
0
votes
0
replies
442
views
iSEE Difference Panel Missing
iSEEu
23 months ago
Dario Strbenac
★ 1.6k
0
votes
1
reply
1.1k
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
23 months ago
isaromero8888
• 0
0
votes
1
reply
680
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 23 months ago by
Ram
▴ 220 • written 23 months ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
1.2k
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 23 months ago by
ATpoint
★ 5.0k • written 23 months ago by
Ömür Koray
• 0
0
votes
2
replies
932
views
TCGA-GBM subtype tumor
curatedTCGAData
updated 23 months ago by
Marcel Ramos
700 • written 23 months ago by
vicmonm5
• 0
0
votes
0
replies
611
views
clusterSweep Warning k Capped
bluster
23 months ago
Dario Strbenac
★ 1.6k
0
votes
0
replies
956
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
23 months ago
Jawahar
• 0
0
votes
0
replies
544
views
How to search for a string in a DNAStringSet dataset?
Biostrings
23 months ago
Angela Michalichyn
• 0
0
votes
0
replies
546
views
rpk per cell saved in SCE object.
SingleCellExperiment
23 months ago
JalapenoCornbread
• 0
0
votes
0
replies
617
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
23 months ago
frueher
• 0
2
votes
2
replies
787
views
How to contact Bioconductor's test host?
Bioconductor
updated 23 months ago by
Hervé Pagès
16k • written 23 months ago by
Marek Gierlinski
▴ 30
2
votes
2
replies
1.6k
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
23 months ago
bd2000
▴ 30
0
votes
0
replies
554
views
RFC: significant changes to ensemblVEP package
VariantAnnotation
ensemblVEP
23 months ago
Vincent J. Carey, Jr.
6.7k
0
votes
0
replies
565
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
23 months ago
Aswathy
• 0
0
votes
1
reply
1.1k
views
DESeq2 multi-factor design and interaction terms
DESeq2
updated 23 months ago by
Michael Love
43k • written 23 months ago by
KW
• 0
0
votes
1
reply
682
views
Conversion of .sf to .rgel format for the salmon processed files with transcript to gene mapping.
RnaSeqSampleSize
updated 23 months ago by
ATpoint
★ 5.0k • written 23 months ago by
Anudev
• 0
1
vote
2
replies
1.2k
views
Access genes associated with GO terms for a topGO object created with gene2GO
topGO
23 months ago
Dan
• 0
0
votes
0
replies
557
views
annotatr rn7?
annotatr
23 months ago
chuanjiao6
• 0
0
votes
1
reply
840
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
23 months ago
WS
• 0
0
votes
1
reply
1.0k
views
Mismatch between MAST DE results and expression dot plot
MAST
mastR
23 months ago
Simon
• 0
0
votes
0
replies
15
views
Spam:
What happens after 99999 in chrome dinosaur game?
Experimental
23 months ago
larsenlola06
0
0
votes
0
replies
812
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
24 months ago
Hai
• 0
0
votes
0
replies
689
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
24 months ago
inna.gur
• 0
0
votes
0
replies
716
views
RN to EC Mapping Not Working for Some Nodes
RStudio
ggkegg
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
Ramirj49
• 0
0
votes
3
replies
749
views
Statistical test
NewWave
written 2.0 years ago by
mario
• 0
2
votes
4
replies
1.2k
views
Different genes expression with limma
DESeq2
DifferentialExpression
limma
updated 23 months ago by
Gordon Smyth
53k • written 2.0 years ago by
michelafrancesconi8
• 0
0
votes
0
replies
1.2k
views
Normalization in methylation analysis
Methylation
minfi
preprocessQuantile
MethylationArrayData
preprocessFunnorm
2.0 years ago
kyj2226
• 0
0
votes
1
reply
800
views
Error in (function (classes, fdef, mtable) : Function 'raster' tag 'logical' cannot find an inheritance method
NewWave
updated 2.0 years ago by
shepherl
4.2k • written 2.0 years ago by
1135296741
• 0
0
votes
2
replies
950
views
EBImage - Selecting parameters for x-ray seed size analysis
EBImage
updated 2.0 years ago by
Wolfgang Huber
★ 13k • written 2.0 years ago by
Brian
• 0
0
votes
6
replies
2.2k
views
flowCore >2.0 read.FCS results in $SPILLOVER error when reading certain FCS files (could it be a warning?)
read.FCS
flowCore
updated 2.0 years ago by
SamGG
▴ 360 • written 2.0 years ago by
das.traveller
• 0
1
vote
2
replies
798
views
Inconsistent results in DiffBind
DiffBind
2.0 years ago
Sam
▴ 10
1
vote
4
replies
6.7k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR
SeuratscRNA
written 2.0 years ago by
Bine
▴ 50
1
vote
2
replies
906
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 3 months ago by
littlefishes20
▴ 10 • written 2.0 years ago by
Miquel
• 0
0
votes
0
replies
701
views
Catalyst::cluster function does NOT produce the same results when setting seed
visua
Visualization
CATALYST
2.1 years ago
elefth.pavlos
▴ 40
1
vote
1
reply
854
views
How to read fcs3.2 files
flowCore
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
Gabriel
▴ 10
8
votes
7
replies
2.4k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 2.1 years ago by
Daniel E. Weeks
▴ 30
0
votes
3
replies
2.7k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 2.1 years ago by
Guido Hooiveld
★ 4.1k • written 2.1 years ago by
Aastha Kapoor
• 0
0
votes
1
reply
661
views
analysis of overexpressed proteins in metaproteomes
Proteomics
ProteoMM
ProteomicsWorkflow
Proteome
written 2.1 years ago by
ary.lech
▴ 10
0
votes
0
replies
576
views
Rgraphviz - exported (toFile) dot file loses colour and label information
Rgraphviz
2.1 years ago
sterlinggunn01
• 0
1
vote
2
replies
1.9k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
2.1 years ago • updated 24 months ago
Levi
• 0
0
votes
0
replies
722
views
multipollutant models
statistics
Regression
r
limma
2.1 years ago
Jitendra
▴ 10
1,000 results • Page
8 of 20
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Comment: Bioinformatician at the Lausanne University Hospital
by
TikTsokaasocissalpc
• 0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
TikTsokaasocissalpc
• 0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Answer: Limma-voom sample weights and impact on DEG numbers
by
Gordon Smyth
53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Answer: wgcna module preseravtion taking too long?
by
ATpoint
★ 5.0k
WGCNA is not a Bioconductor package, you won't get an answer here. Consider biostars.org or the r/bioinformatics reddit. Note that 10 sampl…
Answer: Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCP
by
victor04052024
• 0
You write quite well, and the content is very interesting. I'll provide you a link to my page [granny 2](https://granny2.io).
Votes
Limma-voom sample weights and impact on DEG numbers
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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6.7k
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