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1
vote
4
replies
270
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
5 weeks ago
samuel.channon
• 0
0
votes
2
replies
192
views
Visium RNA
metaMSdata
updated 5 weeks ago by
vvvc360work2
• 0 • written 5 weeks ago by
Karlison
• 0
1
vote
2
replies
265
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 5 weeks ago by
ATpoint
★ 4.0k • written 5 weeks ago by
maximilian.beikirch
• 0
0
votes
0
replies
110
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
5 weeks ago
BID
• 0
1
vote
3
replies
255
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 29 days ago by
mercedeh.movassagh
▴ 10 • written 5 weeks ago by
María
• 0
0
votes
2
replies
212
views
Error in msaFun Cannot open input file. No alignment!
msa
written 5 weeks ago by
Kamil Slowikowski
▴ 30
0
votes
1
reply
189
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 4 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 weeks ago by
Julie
• 0
0
votes
1
reply
170
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
230
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 weeks ago
Sam
▴ 10
0
votes
1
reply
215
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 6 weeks ago by
BioinfoMug
• 0
0
votes
1
reply
188
views
Exact same results in Diffbind with different normalization methods
DiffBind
6 weeks ago • updated 5 weeks ago
red_bricks
▴ 50
0
votes
0
replies
127
views
FELLA plotGraph function won't change the legend
FELLA
6 weeks ago
yuhang
• 0
0
votes
0
replies
137
views
medips-output
ngsReports
MEDIPS
6 weeks ago
subhiksha
• 0
0
votes
0
replies
130
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
6 weeks ago
bocsci11
• 0
0
votes
0
replies
109
views
The graphical interface of FELLA doesn't work
FELLA
6 weeks ago
yuhang
• 0
0
votes
0
replies
128
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
6 weeks ago
jean-christophe.helbling
• 0
0
votes
0
replies
144
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
7 weeks ago
Henry
• 0
0
votes
1
reply
200
views
Rcpp compilation error
Release
Rcpp
updated 7 weeks ago by
ATpoint
★ 4.0k • written 7 weeks ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
165
views
Rain error: invalid annotation of time points
rain
7 weeks ago
mpuli011
• 0
0
votes
0
replies
177
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
7 weeks ago
Felix
• 0
0
votes
0
replies
139
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
7 weeks ago • updated 5 weeks ago
Giovanni Calice
▴ 160
0
votes
0
replies
188
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
Andrew
• 0
0
votes
0
replies
133
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
7 weeks ago
chris2.a.white
• 0
0
votes
0
replies
146
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
8 weeks ago
jk
• 0
0
votes
0
replies
143
views
Can I combine collinear variables into a single value
BatchEffect
limma
8 weeks ago
Harrsha
• 0
0
votes
0
replies
216
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
8 weeks ago
vipul14
• 0
0
votes
0
replies
110
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
8 weeks ago
danalvoronov
▴ 10
0
votes
0
replies
132
views
lfcSE
RGSEA
8 weeks ago
Gordon
• 0
0
votes
4
replies
277
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
8 weeks ago
mperalc
• 0
1
vote
0
replies
158
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
8 weeks ago
BioinfoMug
• 0
0
votes
0
replies
146
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
8 weeks ago
thomas.heigl.ibk
• 0
0
votes
1
reply
240
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 8 weeks ago by
ATpoint
★ 4.0k • written 8 weeks ago by
sodiogoes
• 0
0
votes
6
replies
680
views
StringDB: Cannot finish their tutorial because of an error
STRINGdb
updated 6 weeks ago by
qianyi13
• 0 • written 8 weeks ago by
Pavel
• 0
0
votes
2
replies
303
views
problem in installing the new version of bioconductor
ANCOMBC
updated 9 weeks ago by
shepherl
3.8k • written 9 weeks ago by
Maryam
• 0
0
votes
0
replies
162
views
Comparing the effects of a condition over time in two seperate tissues
MAST
9 weeks ago
Dillon
• 0
0
votes
4
replies
319
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage
rtracklayer
updated 9 weeks ago by
shepherl
3.8k • written 9 weeks ago by
Lucille
• 0
0
votes
3
replies
235
views
problems updating package
TrajectoryGeometry
9 weeks ago
michael.shapiro
• 0
0
votes
0
replies
197
views
how to solve this error?
ChAMPdata
ChAMP
9 weeks ago
Meghana
• 0
1
vote
1
reply
245
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 4 weeks ago by
SamGG
▴ 350 • written 9 weeks ago by
jarod
▴ 30
0
votes
0
replies
150
views
flowAI: flow rare check in R vs FlowJo
flowAI
9 weeks ago
Olena
• 0
0
votes
0
replies
191
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
9 weeks ago
mat149
▴ 70
0
votes
0
replies
156
views
GDC slides download
TCGAbiolinks
10 weeks ago
jain72744
• 0
0
votes
0
replies
208
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
10 weeks ago
Abril
• 0
0
votes
4
replies
279
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 10 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 10 weeks ago by
tirordep
• 0
0
votes
1
reply
207
views
"Counts" in enrichGO
GSEABase
updated 10 weeks ago by
Tyler Sagendorf
▴ 10 • written 11 weeks ago by
Matthew
• 0
0
votes
1
reply
247
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 11 weeks ago by
ATpoint
★ 4.0k • written 11 weeks ago by
Priya
• 0
2
votes
15
replies
663
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 10 weeks ago by
Michael Love
41k • written 11 weeks ago by
cinzia.spagnoli
• 0
0
votes
0
replies
153
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
11 weeks ago
nilanjanamani88
• 0
1
vote
1
reply
214
views
502 error biomaRt getLDS()
ensembldb
biomaRt
updated 10 weeks ago by
Robin
• 0 • written 11 weeks ago by
Pez
▴ 10
0
votes
3
replies
388
views
Unable to install clusterProfiler
clusterProfiler
updated 10 weeks ago by
Perry
• 0 • written 11 weeks ago by
harsh
• 0
1,000 results • Page
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Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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