0
votes
3
replies
327
views
Statistical test
NewWave
written 4 months ago by • 0
1
vote
5
replies
339
views
fgsea fork
fgsea
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
0
votes
0
replies
110
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
5 weeks ago feather-W • 0
0
votes
0
replies
109
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
5 weeks ago Ankit ▴ 20
0
votes
0
replies
96
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
5 weeks ago Pierre Lindenbaum ▴ 10
1
vote
3
replies
272
views
miRTarRnaseq library
miRNATarget mirTarRnaSeq
updated 5 weeks ago by ▴ 10 • written 6 weeks ago by • 0
0
votes
1
reply
197
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 5 weeks ago by ★ 3.9k • written 6 weeks ago by • 0
1
vote
1
reply
260
views
FCS3.2 reading
flowWorkspace flowCore CytoML
updated 5 weeks ago by ▴ 350 • written 11 weeks ago by ▴ 30
3
votes
3
replies
397
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 5 weeks ago by ▴ 160 • written 5 weeks ago by • 0
0
votes
2
replies
570
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 5 weeks ago by • 0 • written 11 months ago by • 0
0
votes
0
replies
119
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
5 weeks ago gshweta95 • 0
2
votes
1
reply
211
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 5 weeks ago by ★ 3.9k • written 6 weeks ago by ▴ 10
0
votes
2
replies
252
views
Error in msaFun Cannot open input file. No alignment!
msa
written 6 weeks ago by ▴ 30
0
votes
0
replies
116
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
6 weeks ago nromerov • 0
1
vote
3
replies
261
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 6 weeks ago by 690 • written 6 weeks ago by • 0
1
vote
4
replies
290
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
6 weeks ago samuel.channon • 0
0
votes
0
replies
131
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray cdf crlmm
6 weeks ago mayra.haedo • 0
0
votes
0
replies
113
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry flowWorkspace flowCore
6 weeks ago taylor.witte • 0
0
votes
0
replies
139
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
6 weeks ago erbrocato • 0
1
vote
2
replies
285
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 6 weeks ago by ★ 4.1k • written 6 weeks ago by • 0
0
votes
2
replies
201
views
Visium RNA
metaMSdata
updated 6 weeks ago by • 0 • written 6 weeks ago by • 0
0
votes
0
replies
116
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
6 weeks ago BID • 0
0
votes
0
replies
148
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
8 weeks ago • updated 6 weeks ago Giovanni Calice ▴ 160
1
vote
2
replies
713
views
gds in GEOmetadb 2023-06-26 version is empty
GEOmetadb
written 10 months ago by ▴ 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 6 weeks ago by ▴ 20 • written 5.2 years ago by • 0
0
votes
1
reply
177
views
Sample-specific methylation values using QSEA
DNAMethylation cfMeDIP-seq cfDNA qsea
updated 6 weeks ago by • 0 • written 12 weeks ago by • 0
0
votes
1
reply
184
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 180
0
votes
1
reply
197
views
Exact same results in Diffbind with different normalization methods
DiffBind
7 weeks ago • updated 6 weeks ago red_bricks ▴ 50
3
votes
1
reply
1.8k
views
TwoSampleMR and ieugwasr
ieugwasr clumping TwoSampleMR
updated 7 weeks ago by ▴ 10 • written 2.1 years ago by ▴ 90
0
votes
1
reply
682
views
gwas power calculation for quantitative traits
power GWAS
written 2.7 years ago by • 0
0
votes
2
replies
244
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago Sam ▴ 10
0
votes
1
reply
227
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks TCGA clinical TCGA-BRCA
written 7 weeks ago by • 0
0
votes
0
replies
134
views
FELLA plotGraph function won't change the legend
FELLA
7 weeks ago yuhang • 0
0
votes
0
replies
147
views
medips-output
ngsReports MEDIPS
7 weeks ago subhiksha • 0
0
votes
0
replies
140
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas db0
7 weeks ago bocsci11 • 0
0
votes
0
replies
114
views
The graphical interface of FELLA doesn't work
FELLA
7 weeks ago yuhang • 0
0
votes
0
replies
132
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
7 weeks ago jean-christophe.helbling • 0
0
votes
6
replies
717
views
StringDB: Cannot finish their tutorial because of an error
STRINGdb
updated 7 weeks ago by • 0 • written 10 weeks ago by • 0
0
votes
1
reply
217
views
Rcpp compilation error
Release Rcpp
updated 8 weeks ago by ★ 4.1k • written 8 weeks ago by ▴ 40
0
votes
0
replies
155
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
8 weeks ago Henry • 0
0
votes
0
replies
175
views
Rain error: invalid annotation of time points
rain
8 weeks ago mpuli011 • 0
0
votes
0
replies
191
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
8 weeks ago Felix • 0
0
votes
1
reply
979
views
ConsensusClusterPlus without figures
clustering
updated 8 weeks ago by • 0 • written 6.5 years ago by • 0
0
votes
0
replies
205
views
Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 8 weeks ago by 65k • written 8 weeks ago by • 0
0
votes
0
replies
143
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
8 weeks ago chris2.a.white • 0
1
vote
1
reply
392
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 8 weeks ago by ▴ 380 • written 3 months ago by ▴ 10
0
votes
1
reply
880
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 9 weeks ago by ▴ 720 • written 15 months ago by • 0
0
votes
0
replies
165
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
149
views
Can I combine collinear variables into a single value
BatchEffect limma
9 weeks ago Harrsha • 0
0
votes
0
replies
233
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
1,000 results • Page 2 of 20
Recent ...
Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to Zainab • 0
Popular Question to Theo ▴ 10
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Locations • All
Ireland, 34 minutes ago
France, 41 minutes ago
France, 54 minutes ago
UPF, Barcelona, Spain, 1 hour ago
Germany, 1 hour ago
Traffic: 495 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