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0
votes
1
reply
196
views
DESeq2 gives an error and R crashes
DESeq2
5 weeks ago
Shefali
• 0
0
votes
0
replies
150
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
5 weeks ago
Eryn
• 0
0
votes
0
replies
96
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
5 weeks ago
Dennis
• 0
0
votes
1
reply
196
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 4 weeks ago by
Guido Hooiveld
★ 4.0k • written 5 weeks ago by
Lucie
• 0
0
votes
0
replies
128
views
ggtree tip label position (depth)
ggtree
5 weeks ago
Roope
• 0
2
votes
6
replies
456
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
6 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
116
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
174
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
fer_talavera
• 0
0
votes
2
replies
279
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
6 weeks ago • updated 28 days ago
isaac.vock
• 0
0
votes
7
replies
435
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
124
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
7 weeks ago
feather-W
• 0
0
votes
0
replies
120
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
7 weeks ago
Ankit
▴ 20
1
vote
5
replies
363
views
fgsea fork
fgsea
updated 6 weeks ago by
James W. MacDonald
65k • written 7 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
3
votes
3
replies
452
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
0
votes
0
replies
139
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
7 weeks ago
gshweta95
• 0
2
votes
1
reply
230
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 7 weeks ago by
Guido Hooiveld
★ 4.0k • written 8 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
700 • 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
312
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
213
views
Visium RNA
metaMSdata
updated 8 weeks ago by
vvvc360work2
• 0 • written 8 weeks ago by
Karlison
• 0
1
vote
2
replies
306
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
281
views
Error in msaFun Cannot open input file. No alignment!
msa
written 8 weeks ago by
Kamil Slowikowski
▴ 30
0
votes
1
reply
204
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
195
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 8 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
271
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 weeks ago
Sam
▴ 10
0
votes
1
reply
250
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
212
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
155
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
9 weeks ago
bocsci11
• 0
0
votes
0
replies
123
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
170
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
10 weeks ago
Henry
• 0
0
votes
1
reply
255
views
Rcpp compilation error
Release
Rcpp
updated 10 weeks ago by
ATpoint
★ 4.1k • written 10 weeks ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
194
views
Rain error: invalid annotation of time points
rain
10 weeks ago
mpuli011
• 0
0
votes
0
replies
217
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
167
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
181
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
11 weeks ago
jk
• 0
1,000 results • Page
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Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters
by
anne-laure
• 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
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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