2
votes
2
replies
194
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago Henry ▴ 10
0
votes
3
replies
290
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 4 weeks ago by ▴ 850 • written 5 weeks ago by • 0
0
votes
0
replies
106
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 weeks ago Stevie Pederson • 0
3
votes
6
replies
315
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
5 weeks ago nhaus ▴ 30
0
votes
1
reply
202
views
DESeq2 gives an error and R crashes
DESeq2
5 weeks ago Shefali • 0
0
votes
0
replies
160
views
LearnTaxa with custom Silva
DECIPHER LearnTaxa
5 weeks ago Eryn • 0
0
votes
0
replies
98
views
queryDGIdb lexical error for some genes
lexicalerror rDGIdb DGIdb json
5 weeks ago Dennis • 0
0
votes
1
reply
204
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
0
votes
0
replies
132
views
ggtree tip label position (depth)
ggtree
6 weeks ago • updated 5 weeks ago Roope • 0
2
votes
6
replies
476
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
6 weeks ago Chris ▴ 10
0
votes
0
replies
165
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
118
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
177
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 7 weeks ago by 66k • written 7 weeks ago by • 0
0
votes
2
replies
318
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR CopyhelpeR
7 weeks ago • updated 6 weeks ago fer_talavera • 0
0
votes
2
replies
285
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
7 weeks ago • updated 4 weeks ago isaac.vock • 0
0
votes
7
replies
450
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
7 weeks ago needNGS • 0
0
votes
0
replies
127
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
7 weeks ago feather-W • 0
0
votes
0
replies
126
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
7 weeks ago Ankit ▴ 20
1
vote
5
replies
372
views
fgsea fork
fgsea
updated 7 weeks ago by 66k • written 7 weeks ago by • 0
0
votes
0
replies
113
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
7 weeks ago Pierre Lindenbaum ▴ 10
3
votes
3
replies
459
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 8 weeks ago by ▴ 160 • written 8 weeks ago by • 0
0
votes
0
replies
144
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
8 weeks ago gshweta95 • 0
2
votes
1
reply
238
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 8 weeks ago by ★ 4.0k • written 8 weeks ago by ▴ 10
0
votes
0
replies
125
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
8 weeks ago nromerov • 0
1
vote
3
replies
276
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 8 weeks ago by 700 • written 8 weeks ago by • 0
0
votes
0
replies
144
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray cdf crlmm
8 weeks ago mayra.haedo • 0
0
votes
0
replies
127
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry flowWorkspace flowCore
8 weeks ago taylor.witte • 0
0
votes
0
replies
153
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
8 weeks ago erbrocato • 0
1
vote
4
replies
318
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
227
views
Visium RNA
metaMSdata
written 8 weeks ago by • 0
1
vote
2
replies
314
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 8 weeks ago by ★ 4.1k • written 8 weeks ago by • 0
0
votes
0
replies
124
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
9 weeks ago BID • 0
1
vote
3
replies
294
views
miRTarRnaseq library
miRNATarget mirTarRnaSeq
updated 7 weeks ago by ▴ 10 • written 9 weeks ago by • 0
0
votes
2
replies
299
views
Error in msaFun Cannot open input file. No alignment!
msa
written 9 weeks ago by ▴ 30
0
votes
1
reply
208
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 7 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
0
votes
1
reply
201
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 9 weeks ago by 50k • written 9 weeks ago by ▴ 180
0
votes
2
replies
281
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
10 weeks ago • updated 9 weeks ago Sam ▴ 10
0
votes
1
reply
255
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks TCGA clinical TCGA-BRCA
written 10 weeks ago by • 0
0
votes
1
reply
222
views
Exact same results in Diffbind with different normalization methods
DiffBind
10 weeks ago • updated 9 weeks ago red_bricks ▴ 50
0
votes
0
replies
142
views
FELLA plotGraph function won't change the legend
FELLA
10 weeks ago yuhang • 0
0
votes
0
replies
174
views
medips-output
ngsReports MEDIPS
10 weeks ago Researcher • 0
0
votes
0
replies
158
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas db0
10 weeks ago bocsci11 • 0
0
votes
0
replies
124
views
The graphical interface of FELLA doesn't work
FELLA
10 weeks ago yuhang • 0
0
votes
0
replies
148
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
10 weeks ago jean-christophe.helbling • 0
0
votes
0
replies
177
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
10 weeks ago Henry • 0
0
votes
1
reply
261
views
Rcpp compilation error
Release Rcpp
updated 10 weeks ago by ★ 4.1k • written 10 weeks ago by ▴ 40
0
votes
0
replies
199
views
Rain error: invalid annotation of time points
rain
10 weeks ago mpuli011 • 0
0
votes
0
replies
224
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
10 weeks ago Felix • 0
1,000 results • Page 2 of 20
Recent ...
Replies
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Comment: ChAMP installation issue by Tahirah • 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Awards • All
Scholar to Mike Smith ★ 6.5k
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to bas_work ▴ 30
Popular Question to landenshanie ▴ 40
Locations • All
United States, just now
United States, 7 minutes ago
Spain, 10 minutes ago
United States, 11 minutes ago
Sweden, 21 minutes ago
Traffic: 714 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6