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0
votes
0
replies
153
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
5 weeks ago
Eryn
• 0
0
votes
0
replies
97
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
5 weeks ago
Dennis
• 0
0
votes
1
reply
199
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 5 weeks ago by
Guido Hooiveld
★ 4.0k • written 5 weeks ago by
Lucie
• 0
0
votes
0
replies
130
views
ggtree tip label position (depth)
ggtree
5 weeks ago
Roope
• 0
2
votes
6
replies
465
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
163
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
146
views
Granges regionCounts not returning the expected number of entries
methylKit
6 weeks ago
Modoc Kesner
▴ 10
0
votes
0
replies
117
views
flowDensity on a flowset
flowDensity
6 weeks ago
fredrikwallberg
• 0
0
votes
0
replies
106
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
6 weeks ago
Macsue
• 0
0
votes
1
reply
176
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
315
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
283
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
6 weeks ago • updated 29 days ago
isaac.vock
• 0
0
votes
7
replies
440
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
7 weeks ago • updated 6 weeks ago
needNGS
• 0
0
votes
0
replies
126
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
7 weeks ago
feather-W
• 0
0
votes
0
replies
124
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
7 weeks ago
Ankit
▴ 20
1
vote
5
replies
368
views
fgsea fork
fgsea
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
yimjohns
• 0
0
votes
0
replies
111
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
7 weeks ago
Pierre Lindenbaum
▴ 10
3
votes
3
replies
456
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 7 weeks ago by
alan.ocallaghan
▴ 160 • written 8 weeks ago by
Najla Abassi
• 0
0
votes
0
replies
141
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
7 weeks ago
gshweta95
• 0
2
votes
1
reply
233
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
271
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
141
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
313
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
214
views
Visium RNA
metaMSdata
updated 8 weeks ago by
vvvc360work2
• 0 • written 8 weeks ago by
Karlison
• 0
1
vote
2
replies
309
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
120
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
8 weeks ago
BID
• 0
1
vote
3
replies
290
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 7 weeks ago by
mercedeh.movassagh
▴ 10 • written 8 weeks ago by
María
• 0
0
votes
2
replies
291
views
Error in msaFun Cannot open input file. No alignment!
msa
written 8 weeks ago by
Kamil Slowikowski
▴ 30
0
votes
1
reply
206
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
199
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
275
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 weeks ago
Sam
▴ 10
0
votes
1
reply
253
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
215
views
Exact same results in Diffbind with different normalization methods
DiffBind
9 weeks ago
red_bricks
▴ 50
0
votes
0
replies
139
views
FELLA plotGraph function won't change the legend
FELLA
9 weeks ago
yuhang
• 0
0
votes
0
replies
172
views
medips-output
ngsReports
MEDIPS
9 weeks ago
Researcher
• 0
0
votes
0
replies
156
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
145
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
9 weeks ago
jean-christophe.helbling
• 0
0
votes
0
replies
173
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
10 weeks ago
Henry
• 0
0
votes
1
reply
257
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
198
views
Rain error: invalid annotation of time points
rain
10 weeks ago
mpuli011
• 0
0
votes
0
replies
219
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
170
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
244
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
183
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
11 weeks ago
jk
• 0
0
votes
0
replies
167
views
Can I combine collinear variables into a single value
BatchEffect
limma
11 weeks ago
Harrsha
• 0
400 results • Page
2 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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Dario Strbenac
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Vincent J. Carey, Jr.
6.7k
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Koen Van den Berge
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