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261
views
Error in set(x, j = name, value = value) : Supplied 52 items to be assigned to 55 items of column 'locus'. If you wish to 'recycle' the RHS please…
ASpli
11 weeks ago
vipul14
• 0
0
votes
0
replies
128
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
11 weeks ago
danalvoronov
▴ 10
0
votes
0
replies
153
views
lfcSE
RGSEA
11 weeks ago
Gordon
• 0
0
votes
4
replies
325
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
189
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
173
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
11 weeks ago
thomas.heigl.ibk
• 0
0
votes
1
reply
267
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 12 weeks ago by
sodiogoes
• 0
0
votes
6
replies
790
views
StringDB: Cannot finish their tutorial because of an error
STRINGdb
updated 9 weeks ago by
qianyi13
• 0 • written 12 weeks ago by
Pavel
• 0
0
votes
2
replies
341
views
problem in installing the new version of bioconductor
ANCOMBC
updated 12 weeks ago by
shepherl
3.9k • written 12 weeks ago by
Maryam
• 0
0
votes
0
replies
179
views
Comparing the effects of a condition over time in two seperate tissues
MAST
12 weeks ago
Dillon
• 0
0
votes
4
replies
412
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
270
views
problems updating package
TrajectoryGeometry
12 weeks ago
michael.shapiro
• 0
0
votes
0
replies
231
views
how to solve this error?
ChAMPdata
ChAMP
3 months ago
Meghana
• 0
1
vote
1
reply
271
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 7 weeks ago by
SamGG
▴ 350 • written 3 months ago by
jarod
▴ 30
0
votes
0
replies
184
views
flowAI: flow rare check in R vs FlowJo
flowAI
3 months 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
180
views
GDC slides download
TCGAbiolinks
3 months ago
jain72744
• 0
0
votes
0
replies
242
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
3 months ago
Abril
• 0
0
votes
4
replies
320
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
238
views
"Counts" in enrichGO
GSEABase
updated 3 months ago by
Tyler Sagendorf
▴ 10 • written 3 months ago by
Matthew
• 0
0
votes
1
reply
318
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
731
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
195
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
3 months ago
nilanjanamani88
• 0
1
vote
1
reply
248
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
459
views
Unable to install clusterProfiler
clusterProfiler
updated 3 months ago by
Perry
• 0 • written 3 months ago by
harsh
• 0
0
votes
0
replies
170
views
rain: Error in peakl[[x]] : subscript out of bounds
rain
3 months ago
mata
• 0
1
vote
5
replies
484
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
192
views
Recount3 error downloading data
recount3
recount
3 months ago
Max Bone
• 0
0
votes
0
replies
144
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
193
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
updated 9 weeks ago by
Simon Pearce
• 0 • written 3 months ago by
User3088
• 0
1
vote
4
replies
507
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
144
views
What is the significance of DMR in DMRcate
DMRcate
3 months ago
chuanjiao6
• 0
0
votes
0
replies
128
views
HiCDCPlus differential interaction error
HiCDCPlus
3 months ago
Irene
• 0
0
votes
0
replies
173
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
3 months ago
Thalita
• 0
1
vote
1
reply
413
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
154
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
268
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
187
views
Annotatr Duplicate Entries
annotatr
AnnotationHub
3 months ago
hayleyw
• 0
0
votes
0
replies
142
views
IlluminaHumanMethylation27kanno.ilmn12.hg19 package is mapped to hg18 genome
IlluminaHumanMethylation27kanno.ilmn12.hg19
3 months ago
Basti
▴ 780
0
votes
0
replies
157
views
iSEE Difference Panel Missing
iSEEu
3 months ago
Dario Strbenac
★ 1.5k
0
votes
1
reply
327
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
260
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
334
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
264
views
TCGA-GBM subtype tumor
curatedTCGAData
updated 3 months ago by
Marcel Ramos
700 • written 3 months ago by
vicmonm5
• 0
0
votes
0
replies
180
views
clusterSweep Warning k Capped
bluster
3 months ago
Dario Strbenac
★ 1.5k
0
votes
0
replies
268
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
175
views
How to search for a string in a DNAStringSet dataset?
Biostrings
4 months ago
Angela Michalichyn
• 0
0
votes
0
replies
175
views
rpk per cell saved in SCE object.
SingleCellExperiment
4 months ago
JalapenoCornbread
• 0
400 results • Page
3 of 8
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Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
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
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3.9k
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