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votes
0
replies
125
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
6 weeks ago
gshweta95
• 0
2
votes
1
reply
214
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 6 weeks ago by
Guido Hooiveld
★ 3.9k • written 6 weeks ago by
enee
▴ 10
0
votes
0
replies
117
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
6 weeks ago
nromerov
• 0
1
vote
3
replies
262
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 6 weeks ago by
Marcel Ramos
690 • written 6 weeks ago by
Astrid Deschênes
• 0
0
votes
0
replies
132
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
6 weeks ago
mayra.haedo
• 0
0
votes
0
replies
115
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
6 weeks ago
taylor.witte
• 0
0
votes
0
replies
141
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
6 weeks ago
erbrocato
• 0
1
vote
4
replies
296
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
6 weeks ago
samuel.channon
• 0
0
votes
2
replies
201
views
Visium RNA
metaMSdata
updated 6 weeks ago by
vvvc360work2
• 0 • written 6 weeks ago by
Karlison
• 0
1
vote
2
replies
292
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 6 weeks ago by
ATpoint
★ 4.1k • written 6 weeks ago by
maximilian.beikirch
• 0
0
votes
0
replies
117
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
7 weeks ago
BID
• 0
1
vote
3
replies
283
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 5 weeks ago by
mercedeh.movassagh
▴ 10 • written 7 weeks ago by
María
• 0
0
votes
2
replies
260
views
Error in msaFun Cannot open input file. No alignment!
msa
written 7 weeks ago by
Kamil Slowikowski
▴ 30
0
votes
1
reply
198
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 5 weeks ago by
Guido Hooiveld
★ 3.9k • written 7 weeks ago by
Julie
• 0
0
votes
1
reply
185
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
253
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
8 weeks ago • updated 7 weeks ago
Sam
▴ 10
0
votes
1
reply
234
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 8 weeks ago by
BioinfoMug
• 0
0
votes
1
reply
200
views
Exact same results in Diffbind with different normalization methods
DiffBind
8 weeks ago • updated 7 weeks ago
red_bricks
▴ 50
0
votes
0
replies
134
views
FELLA plotGraph function won't change the legend
FELLA
8 weeks ago
yuhang
• 0
0
votes
0
replies
152
views
medips-output
ngsReports
MEDIPS
8 weeks ago
subhiksha
• 0
0
votes
0
replies
141
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
8 weeks ago
bocsci11
• 0
0
votes
0
replies
115
views
The graphical interface of FELLA doesn't work
FELLA
8 weeks ago
yuhang
• 0
0
votes
0
replies
136
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
8 weeks ago
jean-christophe.helbling
• 0
0
votes
0
replies
156
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
8 weeks ago
Henry
• 0
0
votes
1
reply
222
views
Rcpp compilation error
Release
Rcpp
updated 8 weeks ago by
ATpoint
★ 4.1k • written 8 weeks ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
176
views
Rain error: invalid annotation of time points
rain
8 weeks ago
mpuli011
• 0
0
votes
0
replies
198
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
8 weeks ago
Felix
• 0
0
votes
0
replies
154
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
9 weeks ago • updated 7 weeks ago
Giovanni Calice
▴ 160
0
votes
0
replies
213
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 9 weeks ago by
James W. MacDonald
65k • written 9 weeks ago by
Andrew
• 0
0
votes
0
replies
148
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
9 weeks ago
chris2.a.white
• 0
0
votes
0
replies
166
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
9 weeks ago
jk
• 0
0
votes
0
replies
153
views
Can I combine collinear variables into a single value
BatchEffect
limma
9 weeks ago
Harrsha
• 0
0
votes
0
replies
238
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
9 weeks ago
vipul14
• 0
0
votes
0
replies
117
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
9 weeks ago
danalvoronov
▴ 10
0
votes
0
replies
144
views
lfcSE
RGSEA
9 weeks ago
Gordon
• 0
0
votes
4
replies
304
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
10 weeks ago • updated 9 weeks ago
mperalc
• 0
1
vote
0
replies
177
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
10 weeks ago
BioinfoMug
• 0
0
votes
0
replies
161
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
10 weeks ago
thomas.heigl.ibk
• 0
0
votes
1
reply
254
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 10 weeks ago by
ATpoint
★ 4.1k • written 10 weeks ago by
sodiogoes
• 0
0
votes
6
replies
739
views
StringDB: Cannot finish their tutorial because of an error
STRINGdb
updated 8 weeks ago by
qianyi13
• 0 • written 10 weeks ago by
Pavel
• 0
0
votes
2
replies
317
views
problem in installing the new version of bioconductor
ANCOMBC
updated 10 weeks ago by
shepherl
3.9k • written 10 weeks ago by
Maryam
• 0
0
votes
0
replies
172
views
Comparing the effects of a condition over time in two seperate tissues
MAST
10 weeks ago
Dillon
• 0
0
votes
4
replies
358
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage
rtracklayer
updated 10 weeks ago by
shepherl
3.9k • written 10 weeks ago by
Lucille
• 0
0
votes
3
replies
252
views
problems updating package
TrajectoryGeometry
10 weeks ago
michael.shapiro
• 0
0
votes
0
replies
217
views
how to solve this error?
ChAMPdata
ChAMP
11 weeks ago
Meghana
• 0
1
vote
1
reply
264
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 6 weeks ago by
SamGG
▴ 350 • written 11 weeks ago by
jarod
▴ 30
0
votes
0
replies
176
views
flowAI: flow rare check in R vs FlowJo
flowAI
11 weeks ago
Olena
• 0
0
votes
0
replies
202
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
11 weeks ago
mat149
▴ 70
0
votes
0
replies
170
views
GDC slides download
TCGAbiolinks
11 weeks ago
jain72744
• 0
0
votes
0
replies
226
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
11 weeks ago
Abril
• 0
1,000 results • Page
2 of 20
Recent ...
Replies
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark?
by
Juan Higareda
• 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance
by
James W. MacDonald
65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip
by
James W. MacDonald
65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
Votes
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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