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Creation
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Views
Votes
0
votes
0
replies
102
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 weeks ago
Stevie Pederson
• 0
0
votes
1
reply
194
views
DESeq2 gives an error and R crashes
DESeq2
5 weeks ago
Shefali
• 0
3
votes
6
replies
304
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
5 weeks ago
nhaus
▴ 30
0
votes
0
replies
149
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
359
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 5 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 7 months ago by
karmasstark
• 0
0
votes
0
replies
126
views
ggtree tip label position (depth)
ggtree
5 weeks ago
Roope
• 0
0
votes
1
reply
519
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 5 weeks ago by
ivorychan7777
• 0 • written 15 months ago by
609b0d25
• 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
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
1
reply
558
views
CopywriteR output
CopywriteR
updated 5 weeks ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 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
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
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
7
replies
434
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
3
replies
341
views
Statistical test
NewWave
written 4 months ago by
mario
• 0
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
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
0
votes
0
replies
109
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
7 weeks ago
Pierre Lindenbaum
▴ 10
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
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
1
vote
1
reply
269
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 7 weeks ago by
SamGG
▴ 350 • written 12 weeks ago by
jarod
▴ 30
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
0
votes
2
replies
585
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 7 weeks ago by
CHEN
• 0 • written 12 months ago by
Saanchi
• 0
0
votes
0
replies
138
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
7 weeks ago
gshweta95
• 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
2
replies
280
views
Error in msaFun Cannot open input file. No alignment!
msa
written 8 weeks ago by
Kamil Slowikowski
▴ 30
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
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
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
2
replies
305
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
2
replies
213
views
Visium RNA
metaMSdata
updated 8 weeks ago by
vvvc360work2
• 0 • written 8 weeks ago by
Karlison
• 0
0
votes
0
replies
119
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
8 weeks ago
BID
• 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
1
vote
2
replies
737
views
gds in GEOmetadb 2023-06-26 version is empty
GEOmetadb
written 10 months ago by
malat1_t
▴ 10
0
votes
1
reply
1.1k
views
How can I compute AIC for MAST hurdle model fitted in the whole dataset?
MAST
AIC calcuation
Parameters
single cell
hurdle model
updated 8 weeks ago by
rproendo
▴ 20 • written 5.3 years ago by
mcalgaro93
• 0
0
votes
1
reply
189
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
updated 8 weeks ago by
Simon Pearce
• 0 • written 3 months ago by
User3088
• 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
1
reply
212
views
Exact same results in Diffbind with different normalization methods
DiffBind
9 weeks ago • updated 8 weeks ago
red_bricks
▴ 50
3
votes
1
reply
1.9k
views
TwoSampleMR and ieugwasr
ieugwasr
clumping
TwoSampleMR
updated 8 weeks ago by
zoheir.alayash
▴ 10 • written 2.2 years ago by
S T
▴ 90
0
votes
1
reply
686
views
gwas power calculation for quantitative traits
power
GWAS
written 2.7 years ago by
rajya82
• 0
0
votes
2
replies
271
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 weeks ago
Sam
▴ 10
0
votes
1
reply
249
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
0
replies
138
views
FELLA plotGraph function won't change the legend
FELLA
9 weeks ago
yuhang
• 0
1,000 results • Page
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Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning
by
angelaesper43
• 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
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…
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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