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0
votes
4
replies
321
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
11 weeks ago
mperalc
• 0
1
vote
0
replies
186
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
11 weeks ago
BioinfoMug
• 0
0
votes
0
replies
171
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
11 weeks ago
thomas.heigl.ibk
• 0
0
votes
1
reply
263
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 11 weeks ago by
ATpoint
★ 4.1k • written 11 weeks ago by
sodiogoes
• 0
0
votes
6
replies
776
views
StringDB: Cannot finish their tutorial because of an error
STRINGdb
updated 9 weeks ago by
qianyi13
• 0 • written 11 weeks ago by
Pavel
• 0
0
votes
2
replies
334
views
problem in installing the new version of bioconductor
ANCOMBC
updated 11 weeks ago by
shepherl
3.9k • written 12 weeks ago by
Maryam
• 0
0
votes
0
replies
177
views
Comparing the effects of a condition over time in two seperate tissues
MAST
12 weeks ago
Dillon
• 0
0
votes
4
replies
402
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage
rtracklayer
updated 12 weeks ago by
shepherl
3.9k • written 12 weeks ago by
Lucille
• 0
0
votes
3
replies
265
views
problems updating package
TrajectoryGeometry
12 weeks ago
michael.shapiro
• 0
0
votes
0
replies
228
views
how to solve this error?
ChAMPdata
ChAMP
12 weeks ago
Meghana
• 0
1
vote
1
reply
269
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 7 weeks ago by
SamGG
▴ 350 • written 12 weeks ago by
jarod
▴ 30
0
votes
0
replies
182
views
flowAI: flow rare check in R vs FlowJo
flowAI
3 months ago • updated 12 weeks ago
Olena
• 0
0
votes
0
replies
211
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
3 months ago
mat149
▴ 70
0
votes
0
replies
179
views
GDC slides download
TCGAbiolinks
3 months ago
jain72744
• 0
0
votes
0
replies
241
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
3 months ago
Abril
• 0
0
votes
4
replies
317
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 3 months ago by
Lluís Revilla Sancho
▴ 730 • written 3 months ago by
tirordep
• 0
0
votes
1
reply
234
views
"Counts" in enrichGO
GSEABase
updated 3 months ago by
Tyler Sagendorf
▴ 10 • written 3 months ago by
Matthew
• 0
0
votes
1
reply
311
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 3 months ago by
ATpoint
★ 4.1k • written 3 months ago by
Priya
• 0
2
votes
15
replies
727
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 3 months ago by
Michael Love
42k • written 3 months ago by
cinzia.spagnoli
• 0
0
votes
0
replies
190
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
3 months ago
nilanjanamani88
• 0
1
vote
1
reply
241
views
502 error biomaRt getLDS()
ensembldb
biomaRt
updated 3 months ago by
Robin
• 0 • written 3 months ago by
Pez
▴ 10
0
votes
3
replies
447
views
Unable to install clusterProfiler
clusterProfiler
updated 3 months ago by
Perry
• 0 • written 3 months ago by
harsh
• 0
0
votes
0
replies
169
views
rain: Error in peakl[[x]] : subscript out of bounds
rain
3 months ago
mata
• 0
1
vote
5
replies
469
views
BiomaRt download data error
biomaRt
updated 3 months ago by
Mike Smith
★ 6.5k • written 3 months ago by
Max Bone
• 0
0
votes
0
replies
191
views
Recount3 error downloading data
recount3
recount
3 months ago
Max Bone
• 0
0
votes
0
replies
143
views
addcrispraiscores - crisprverse not working
crisprDesign
3 months ago
jimjacob08
• 0
0
votes
0
replies
144
views
Error reading bam files with getCounts after updating R
chromVAR
chrom
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
tsourkas
• 0
0
votes
1
reply
188
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
updated 8 weeks ago by
Simon Pearce
• 0 • written 3 months ago by
User3088
• 0
1
vote
4
replies
500
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
3 months ago
mikat
• 0
0
votes
0
replies
140
views
What is the significance of DMR in DMRcate
DMRcate
3 months ago
chuanjiao6
• 0
0
votes
0
replies
127
views
HiCDCPlus differential interaction error
HiCDCPlus
3 months ago
Irene
• 0
0
votes
0
replies
171
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
3 months ago
Thalita
• 0
1
vote
1
reply
410
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 10 weeks ago by
Yang Liao
▴ 380 • written 3 months ago by
Joe Marturano
▴ 10
0
votes
0
replies
152
views
Postdoc
TCGAWorkflow
3 months ago
sameerahmadguru
• 0
2
votes
6
replies
1.1k
views
Looking for documentation about the use of "split = .sign" in enrichplot's dotplot
enrichplot
3 months ago • updated 12 weeks ago
Tobias
• 0
1
vote
1
reply
264
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 3 months ago by
alan.ocallaghan
▴ 160 • written 3 months ago by
Dario Strbenac
★ 1.5k
0
votes
0
replies
183
views
Annotatr Duplicate Entries
annotatr
AnnotationHub
3 months ago
hayleyw
• 0
0
votes
0
replies
140
views
IlluminaHumanMethylation27kanno.ilmn12.hg19 package is mapped to hg18 genome
IlluminaHumanMethylation27kanno.ilmn12.hg19
3 months ago
Basti
▴ 780
0
votes
0
replies
156
views
iSEE Difference Panel Missing
iSEEu
3 months ago
Dario Strbenac
★ 1.5k
0
votes
1
reply
323
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
3 months ago
isaromero8888
• 0
0
votes
1
reply
252
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 3 months ago by
Ram
▴ 210 • written 3 months ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
327
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 3 months ago by
ATpoint
★ 4.1k • written 3 months ago by
Ömür Koray
• 0
0
votes
2
replies
262
views
TCGA-GBM subtype tumor
curatedTCGAData
updated 3 months ago by
Marcel Ramos
690 • written 3 months ago by
vicmonm5
• 0
0
votes
0
replies
178
views
clusterSweep Warning k Capped
bluster
3 months ago
Dario Strbenac
★ 1.5k
0
votes
0
replies
265
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
3 months ago
Jawahar
• 0
0
votes
0
replies
173
views
How to search for a string in a DNAStringSet dataset?
Biostrings
3 months ago
Angela Michalichyn
• 0
0
votes
0
replies
167
views
rpk per cell saved in SCE object.
SingleCellExperiment
3 months ago
JalapenoCornbread
• 0
0
votes
0
replies
187
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
3 months ago
frueher
• 0
2
votes
2
replies
329
views
How to contact Bioconductor's test host?
Bioconductor
updated 4 months ago by
Hervé Pagès
16k • written 4 months ago by
Marek Gierlinski
▴ 30
2
votes
2
replies
681
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
4 months ago
bd2000
▴ 30
1,000 results • Page
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Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
Matthew Thornton
▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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