0
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0
replies
126
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ggtree tip label position (depth)
ggtree
5 weeks ago Roope • 0
2
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6
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451
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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
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161
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Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
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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
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0
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115
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flowDensity on a flowset
flowDensity
6 weeks ago fredrikwallberg • 0
0
votes
0
replies
104
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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
278
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
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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
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
6 weeks ago feather-W • 0
0
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0
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120
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PCA plot for normalized counts using Diffbind
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6 weeks ago Ankit ▴ 20
1
vote
5
replies
363
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fgsea fork
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updated 6 weeks ago by 65k • written 7 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
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450
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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
229
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
124
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Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
8 weeks ago nromerov • 0
1
vote
3
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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
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140
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crlmm: CDF for Infinium Global Diversity Array By Illumina
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8 weeks ago mayra.haedo • 0
0
votes
0
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124
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Macsquant FCS in read.FCS & opencyto
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8 weeks ago taylor.witte • 0
0
votes
0
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150
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
8 weeks ago erbrocato • 0
1
vote
4
replies
310
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
8 weeks ago samuel.channon • 0
0
votes
2
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213
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Visium RNA
metaMSdata
updated 8 weeks ago by • 0 • written 8 weeks ago by • 0
1
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2
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305
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Extracting genomic sequences using agat and bedtools yields different results
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updated 8 weeks ago by ★ 4.1k • written 8 weeks ago by • 0
0
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0
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119
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DNAcopy segment function not reproducible even when setting seed
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8 weeks ago BID • 0
1
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3
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289
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miRTarRnaseq library
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updated 7 weeks ago by ▴ 10 • written 8 weeks ago by • 0
0
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2
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280
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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
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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
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270
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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.
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0
votes
1
reply
212
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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
138
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FELLA plotGraph function won't change the legend
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9 weeks ago yuhang • 0
0
votes
0
replies
165
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medips-output
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9 weeks ago Researcher • 0
0
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0
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154
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Join BOC Sciences at Drug Discovery Chemistry
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9 weeks ago bocsci11 • 0
0
votes
0
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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
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142
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DEXSeq plot error
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9 weeks ago jean-christophe.helbling • 0
0
votes
0
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To analyze StringTie data using the isoformSwitchAnalyzeR package
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9 weeks ago Henry • 0
0
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1
reply
254
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Rcpp compilation error
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updated 9 weeks ago by ★ 4.1k • written 10 weeks ago by ▴ 40
0
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0
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193
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Rain error: invalid annotation of time points
rain
10 weeks ago mpuli011 • 0
0
votes
0
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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
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0
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166
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TCGAbiolinks STAD project 450k Methylation Beta Value data
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10 weeks ago • updated 8 weeks ago Giovanni Calice ▴ 160
0
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0
replies
239
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Error: grouping factors must have > 1 sampled level
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updated 10 weeks ago by 65k • written 10 weeks ago by • 0
0
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0
replies
158
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Feature Counts -R XS Read Assignment Tag
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10 weeks ago chris2.a.white • 0
0
votes
0
replies
180
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Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
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10 weeks ago jk • 0
0
votes
0
replies
163
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Can I combine collinear variables into a single value
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10 weeks ago Harrsha • 0
0
votes
0
replies
257
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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
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Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
11 weeks ago danalvoronov ▴ 10
0
votes
0
replies
152
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lfcSE
RGSEA
11 weeks ago Gordon • 0
1,000 results • Page 2 of 20
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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!!
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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
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