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0
votes
0
replies
126
views
ggtree tip label position (depth)
ggtree
5 weeks ago
Roope
• 0
2
votes
6
replies
451
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
5 weeks ago
Chris
▴ 10
0
votes
0
replies
161
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
5 weeks ago
andromeda
• 0
0
votes
1
reply
142
views
Granges regionCounts not returning the expected number of entries
methylKit
6 weeks ago • updated 5 weeks ago
Modoc Kesner
▴ 10
0
votes
0
replies
115
views
flowDensity on a flowset
flowDensity
6 weeks ago
fredrikwallberg
• 0
0
votes
0
replies
104
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
6 weeks ago
Macsue
• 0
0
votes
1
reply
173
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
ja569116
• 0
0
votes
2
replies
314
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
6 weeks ago • updated 5 weeks ago
fer_talavera
• 0
0
votes
2
replies
277
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
6 weeks ago • updated 27 days ago
isaac.vock
• 0
0
votes
7
replies
433
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
6 weeks ago
needNGS
• 0
0
votes
0
replies
123
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
6 weeks ago
feather-W
• 0
0
votes
0
replies
120
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
6 weeks ago
Ankit
▴ 20
1
vote
5
replies
363
views
fgsea fork
fgsea
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
yimjohns
• 0
0
votes
0
replies
109
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
7 weeks ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
138
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
7 weeks ago
gshweta95
• 0
3
votes
3
replies
450
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 7 weeks ago by
alan.ocallaghan
▴ 160 • written 7 weeks ago by
Najla Abassi
• 0
2
votes
1
reply
229
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 7 weeks ago by
Guido Hooiveld
★ 4.0k • written 7 weeks ago by
enee
▴ 10
0
votes
0
replies
124
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
8 weeks ago
nromerov
• 0
1
vote
3
replies
269
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 8 weeks ago by
Marcel Ramos
690 • written 8 weeks ago by
Astrid Deschênes
• 0
0
votes
0
replies
140
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
8 weeks ago
mayra.haedo
• 0
0
votes
0
replies
124
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
8 weeks ago
taylor.witte
• 0
0
votes
0
replies
150
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
8 weeks ago
erbrocato
• 0
1
vote
4
replies
310
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
8 weeks ago
samuel.channon
• 0
0
votes
2
replies
212
views
Visium RNA
metaMSdata
updated 8 weeks ago by
vvvc360work2
• 0 • written 8 weeks ago by
Karlison
• 0
1
vote
2
replies
304
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 8 weeks ago by
ATpoint
★ 4.1k • written 8 weeks ago by
maximilian.beikirch
• 0
0
votes
0
replies
119
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
8 weeks ago
BID
• 0
1
vote
3
replies
289
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 7 weeks ago by
mercedeh.movassagh
▴ 10 • written 8 weeks ago by
María
• 0
0
votes
2
replies
280
views
Error in msaFun Cannot open input file. No alignment!
msa
written 8 weeks ago by
Kamil Slowikowski
▴ 30
0
votes
1
reply
203
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 7 weeks ago by
Guido Hooiveld
★ 4.0k • written 8 weeks ago by
Julie
• 0
0
votes
1
reply
194
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
269
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 weeks ago
Sam
▴ 10
0
votes
1
reply
248
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 9 weeks ago by
BioinfoMug
• 0
0
votes
1
reply
211
views
Exact same results in Diffbind with different normalization methods
DiffBind
9 weeks ago • updated 8 weeks ago
red_bricks
▴ 50
0
votes
0
replies
138
views
FELLA plotGraph function won't change the legend
FELLA
9 weeks ago
yuhang
• 0
0
votes
0
replies
165
views
medips-output
ngsReports
MEDIPS
9 weeks ago
Researcher
• 0
0
votes
0
replies
154
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
9 weeks ago
bocsci11
• 0
0
votes
0
replies
122
views
The graphical interface of FELLA doesn't work
FELLA
9 weeks ago
yuhang
• 0
0
votes
0
replies
142
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
9 weeks ago
jean-christophe.helbling
• 0
0
votes
0
replies
168
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
9 weeks ago
Henry
• 0
0
votes
1
reply
254
views
Rcpp compilation error
Release
Rcpp
updated 9 weeks ago by
ATpoint
★ 4.1k • written 10 weeks ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
193
views
Rain error: invalid annotation of time points
rain
10 weeks ago
mpuli011
• 0
0
votes
0
replies
216
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
10 weeks ago
Felix
• 0
0
votes
0
replies
166
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
10 weeks ago • updated 8 weeks ago
Giovanni Calice
▴ 160
0
votes
0
replies
239
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 10 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
Andrew
• 0
0
votes
0
replies
158
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
10 weeks ago
chris2.a.white
• 0
0
votes
0
replies
180
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
10 weeks ago
jk
• 0
0
votes
0
replies
163
views
Can I combine collinear variables into a single value
BatchEffect
limma
10 weeks ago
Harrsha
• 0
0
votes
0
replies
257
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
125
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
11 weeks ago
danalvoronov
▴ 10
0
votes
0
replies
152
views
lfcSE
RGSEA
11 weeks ago
Gordon
• 0
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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