0
votes
0
replies
126
views
ggtree tip label position (depth)
ggtree
5 weeks ago Roope • 0
2
votes
6
replies
450
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
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
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
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 65k • written 6 weeks ago by • 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
2
replies
277
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
6 weeks ago • updated 27 days ago isaac.vock • 0
0
votes
7
replies
433
views
Internet connection for Bioconductor packages in Rstudio in Iran...
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6 weeks ago needNGS • 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
1
vote
5
replies
362
views
fgsea fork
fgsea
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
votes
0
replies
109
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
7 weeks ago Pierre Lindenbaum ▴ 10
3
votes
3
replies
448
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
138
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
7 weeks ago gshweta95 • 0
2
votes
1
reply
228
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 7 weeks ago by ★ 4.0k • written 7 weeks ago by ▴ 10
0
votes
0
replies
123
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
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cBioPortalData loads empty z-score expression table
cBioPortalData
updated 8 weeks ago by 690 • 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
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Macsquant FCS in read.FCS & opencyto
FlowCytometry flowWorkspace flowCore
8 weeks ago taylor.witte • 0
0
votes
0
replies
149
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
8 weeks ago erbrocato • 0
1
vote
4
replies
310
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
212
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Visium RNA
metaMSdata
updated 8 weeks ago by • 0 • written 8 weeks ago by • 0
1
vote
2
replies
304
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
119
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DNAcopy segment function not reproducible even when setting seed
DNAcopy
8 weeks ago BID • 0
1
vote
3
replies
289
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miRTarRnaseq library
miRNATarget mirTarRnaSeq
updated 7 weeks ago by ▴ 10 • written 8 weeks ago by • 0
0
votes
2
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279
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Error in msaFun Cannot open input file. No alignment!
msa
written 8 weeks ago by ▴ 30
0
votes
1
reply
203
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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
194
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Rsubread: buildindex() should support multiple reference files
Rsubread
updated 8 weeks ago by 50k • written 8 weeks ago by ▴ 180
0
votes
2
replies
269
views
Scores used for DiffBind's dba.plotHeatmap
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9 weeks ago Sam ▴ 10
0
votes
1
reply
248
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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
211
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Exact same results in Diffbind with different normalization methods
DiffBind
9 weeks ago • updated 8 weeks ago red_bricks ▴ 50
0
votes
0
replies
137
views
FELLA plotGraph function won't change the legend
FELLA
9 weeks ago yuhang • 0
0
votes
0
replies
165
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medips-output
ngsReports MEDIPS
9 weeks ago Researcher • 0
0
votes
0
replies
154
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Join BOC Sciences at Drug Discovery Chemistry
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9 weeks ago bocsci11 • 0
0
votes
0
replies
122
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The graphical interface of FELLA doesn't work
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9 weeks ago yuhang • 0
0
votes
0
replies
142
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DEXSeq plot error
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9 weeks ago jean-christophe.helbling • 0
0
votes
0
replies
167
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To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
9 weeks ago Henry • 0
0
votes
1
reply
254
views
Rcpp compilation error
Release Rcpp
updated 9 weeks ago by ★ 4.1k • written 10 weeks ago by ▴ 40
0
votes
0
replies
192
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Rain error: invalid annotation of time points
rain
10 weeks ago mpuli011 • 0
0
votes
0
replies
216
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Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
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10 weeks ago Felix • 0
0
votes
0
replies
166
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
238
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
180
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag SplicedAlignment SGSeq minimap2
10 weeks ago jk • 0
0
votes
0
replies
163
views
Can I combine collinear variables into a single value
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10 weeks ago Harrsha • 0
0
votes
0
replies
256
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
11 weeks ago vipul14 • 0
0
votes
0
replies
125
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
11 weeks ago danalvoronov ▴ 10
0
votes
0
replies
152
views
lfcSE
RGSEA
11 weeks ago Gordon • 0
399 results • Page 2 of 8
Recent ...
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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…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
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
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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