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 4 weeks ago by ★ 4.0k • written 5 weeks ago by • 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
145
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 65k • written 6 weeks ago by • 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 65k • written 7 weeks ago by • 0
0
votes
0
replies
110
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 ▴ 160 • written 7 weeks ago by • 0
0
votes
0
replies
140
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 ★ 4.0k • written 8 weeks ago by ▴ 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 700 • written 8 weeks ago by • 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
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 • 0 • written 8 weeks ago by • 0
1
vote
2
replies
308
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
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 ▴ 10 • written 8 weeks ago by • 0
0
votes
2
replies
290
views
Error in msaFun Cannot open input file. No alignment!
msa
written 8 weeks ago by ▴ 30
0
votes
1
reply
206
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 7 weeks ago by ★ 4.0k • written 8 weeks ago by • 0
0
votes
1
reply
199
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
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 • 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
171
views
medips-output
ngsReports MEDIPS
9 weeks ago Researcher • 0
0
votes
0
replies
156
views
Join BOC Sciences at Drug Discovery Chemistry
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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 ★ 4.1k • written 10 weeks ago by ▴ 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
168
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
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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 65k • written 10 weeks ago by • 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
401 results • Page 2 of 9
Recent ...
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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!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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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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