0
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0
replies
114
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror IsoCorrectoR
6 weeks ago Maliha Tabassum • 0
0
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1
reply
145
views
what is the sampleFiles
chipseq
updated 6 weeks ago by 66k • written 6 weeks ago by • 0
0
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0
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114
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
6 weeks ago Virangika • 0
0
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0
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92
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[ChIPseeker] Unable to perform gene ontology analysis
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6 weeks ago Henry ▴ 10
0
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1
reply
160
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Deseq2 Rlog transformation
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updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
2
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2
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205
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[DiffBind] Obtaining normalization factors
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6 weeks ago Henry ▴ 10
0
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3
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299
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A ComBat-seq issue: the covariates are confounded
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updated 5 weeks ago by ▴ 850 • written 6 weeks ago by • 0
0
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0
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109
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
6 weeks ago Stevie Pederson • 0
3
votes
6
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326
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
6 weeks ago nhaus ▴ 40
0
votes
1
reply
208
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DESeq2 gives an error and R crashes
DESeq2
7 weeks ago • updated 6 weeks ago Shefali • 0
0
votes
0
replies
165
views
LearnTaxa with custom Silva
DECIPHER LearnTaxa
7 weeks ago Eryn • 0
0
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0
replies
102
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queryDGIdb lexical error for some genes
lexicalerror rDGIdb DGIdb json
7 weeks ago Dennis • 0
0
votes
1
reply
228
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 6 weeks ago by ★ 4.0k • written 7 weeks ago by • 0
0
votes
0
replies
139
views
ggtree tip label position (depth)
ggtree
7 weeks ago Roope • 0
2
votes
6
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517
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
7 weeks ago Chris ▴ 10
0
votes
0
replies
169
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
7 weeks ago andromeda • 0
0
votes
1
reply
149
views
Granges regionCounts not returning the expected number of entries
methylKit
7 weeks ago Modoc Kesner ▴ 10
0
votes
0
replies
122
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flowDensity on a flowset
flowDensity
7 weeks ago fredrikwallberg • 0
0
votes
0
replies
110
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DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
7 weeks ago Macsue • 0
0
votes
1
reply
178
views
No output from read.bismark with bismark cov.files
bsseq methylation
updated 8 weeks ago by 66k • written 8 weeks ago by • 0
0
votes
2
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323
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Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
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8 weeks ago • updated 7 weeks ago fer_talavera • 0
0
votes
2
replies
292
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
8 weeks ago • updated 5 weeks ago isaac.vock • 0
0
votes
7
replies
465
views
Internet connection for Bioconductor packages in Rstudio in Iran...
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8 weeks ago needNGS • 0
0
votes
0
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130
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
8 weeks ago feather-W • 0
0
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0
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133
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
8 weeks ago Ankit ▴ 20
1
vote
5
replies
386
views
fgsea fork
fgsea
updated 8 weeks ago by 66k • written 8 weeks ago by • 0
0
votes
0
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119
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
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8 weeks ago Pierre Lindenbaum ▴ 10
0
votes
0
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157
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Using Granges to find overlapping pairs at exactly 10kb distance
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9 weeks ago gshweta95 • 0
3
votes
3
replies
481
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 9 weeks ago by ▴ 160 • written 9 weeks ago by • 0
2
votes
1
reply
255
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 9 weeks ago by ★ 4.0k • written 9 weeks ago by ▴ 10
0
votes
0
replies
130
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Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
9 weeks ago nromerov • 0
1
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3
replies
284
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cBioPortalData loads empty z-score expression table
cBioPortalData
updated 9 weeks ago by 700 • written 9 weeks ago by • 0
0
votes
0
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151
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crlmm: CDF for Infinium Global Diversity Array By Illumina
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10 weeks ago mayra.haedo • 0
0
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0
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161
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
10 weeks ago erbrocato • 0
1
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4
replies
331
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
10 weeks ago • updated 9 weeks ago samuel.channon • 0
0
votes
2
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240
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Visium RNA
metaMSdata
written 10 weeks ago by • 0
1
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2
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337
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Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 10 weeks ago by ★ 4.2k • written 10 weeks ago by • 0
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0
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127
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DNAcopy segment function not reproducible even when setting seed
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10 weeks ago BID • 0
2
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3
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310
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miRTarRnaseq library
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updated 8 weeks ago by ▴ 20 • written 10 weeks ago by • 0
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Error in msaFun Cannot open input file. No alignment!
msa
written 10 weeks ago by ▴ 30
0
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1
reply
216
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Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 9 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
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209
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Rsubread: buildindex() should support multiple reference files
Rsubread
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 180
0
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Scores used for DiffBind's dba.plotHeatmap
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11 weeks ago • updated 10 weeks ago Sam ▴ 10
0
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1
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268
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TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
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written 11 weeks ago by • 0
0
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1
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226
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Exact same results in Diffbind with different normalization methods
DiffBind
11 weeks ago • updated 10 weeks ago red_bricks ▴ 50
0
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0
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151
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FELLA plotGraph function won't change the legend
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11 weeks ago yuhang • 0
0
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0
replies
186
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medips-output
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11 weeks ago Researcher • 0
0
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0
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164
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11 weeks ago bocsci11 • 0
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0
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The graphical interface of FELLA doesn't work
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11 weeks ago yuhang • 0
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DEXSeq plot error
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11 weeks ago jean-christophe.helbling • 0
403 results • Page 2 of 9
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Comment: How to run allelic imbalance in apeglm by parayod376 • 0
Which I care about. [Papa's games][1] thank you for sharing the information. [1]: https://papasgamesfree.github.io
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
FYI, I emailed Benilton and he says he's working on a fix, so stay tuned!
Answer: Error in render R qmd document (could not find function "process") by James W. MacDonald 66k
If you have functions in another R document, you have to `source` that document to load the functions into your workspace. Just like you wo…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
For some reason, that's still not working for me on command line. I ended up figuring out another way around, though, by converting the g…
Votes
Reduce the number of nodes appear in the cnetplot of clusterprofiler
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
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