2
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2
replies
412
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Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
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9 days ago • updated 5 days ago Matthew Thornton ▴ 360
0
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188
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Differential gene expression analysis results
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updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
0
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0
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88
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11 days ago neilzhao ▴ 30
0
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1
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116
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normalization using Deseq2
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updated 12 days ago by ★ 4.1k • written 12 days ago by • 0
1
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2
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291
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
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12 days ago • updated 11 days ago Dylan.Sheerin • 0
2
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7
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429
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deseq2 results
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13 days ago • updated 10 days ago sajadahmad41454 • 0
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79
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Treeio as.treedata function seq lenght error
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13 days ago nromerov • 0
2
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2
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287
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
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14 days ago • updated 8 days ago zzrammal • 0
3
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10
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494
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Extremely small p-values using Limma for proteomic data
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updated 11 days ago by 66k • written 14 days ago by • 0
0
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1
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122
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Recovering my account credentials on Bioconductor
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updated 14 days ago by 3.9k • written 14 days ago by • 0
2
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1
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191
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minfi latest update for EPIC V2 chip
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updated 14 days ago by 66k • written 14 days ago by • 0
0
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0
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100
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need help with Diffbind multiple groups
DiffBind ChIPSeqData
14 days ago Dinesh • 0
3
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5
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307
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Help with running egsea()
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15 days ago • updated 13 days ago Chris ▴ 10
3
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1
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157
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How to save the DEXSeq results
DEXSeq
updated 15 days ago by 42k • written 15 days ago by • 0
2
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1
reply
150
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 15 days ago by 42k • written 15 days ago by ▴ 70
0
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3
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238
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Couldn't connect to server while using "pathways"
graphite
updated 14 days ago by 42k • written 15 days ago by • 0
4
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5
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344
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Method to find pathways different between 2 groups
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15 days ago • updated 6 days ago Chris ▴ 10
7
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6
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645
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 15 days ago by • 0
2
votes
2
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238
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fgsea significant result
fgsea
16 days ago Chris ▴ 10
1
vote
2
replies
410
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 17 days ago by 50k • written 17 days ago by • 0
2
votes
3
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287
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package goseq seems to be not available on the latest version of R
goseq
updated 15 days ago by 50k • written 17 days ago by ▴ 20
2
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3
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264
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Too many significant genes when integrating gtex and tcga
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updated 16 days ago by ★ 4.1k • written 18 days ago by • 0
1
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1
reply
196
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Handling multiple differential expression comparisons
DESeq2
updated 16 days ago by 42k • written 18 days ago by ▴ 10
0
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0
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125
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dba.plotProfile() plotting and interpretation
DiffBind
18 days ago Henry ▴ 10
0
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6
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309
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Once again a "Model matrix not full rank"
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updated 17 days ago by ★ 1.4k • written 18 days ago by ▴ 130
4
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2
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643
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
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18 days ago • updated 15 days ago gene_bioconductor ▴ 10
0
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1
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181
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 18 days ago by 50k • written 19 days ago by • 0
0
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1
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166
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Gene-by-sample covariates in limma
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updated 18 days ago by 50k • written 19 days ago by • 0
0
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0
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flowStats for CyTOF
flowStats
19 days ago tholmes • 0
0
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2
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175
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DESeq2 v1.35.0
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updated 19 days ago by 42k • written 19 days ago by • 0
0
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0
replies
97
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DiffBind: no peaks in DBA object
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19 days ago yvonneh • 0
0
votes
0
replies
89
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How to create consensus peak sets for each group to use in DiffBind?
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19 days ago Ian D. ▴ 70
0
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1
reply
145
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 19 days ago by • 0
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2
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219
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Deseq2 and Normalization of RNA sequencing data
DESeq2
19 days ago • updated 18 days ago kcarey • 0
0
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3
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230
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Differences in differential analysis methods for RNA-Seq
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updated 19 days ago by ★ 4.1k • written 19 days ago by • 0
1
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3
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310
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 13 days ago by ★ 4.1k • written 19 days ago by • 0
4
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0
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147
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News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
19 days ago shepherl 3.9k
0
votes
0
replies
142
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Empty table plot using plotGseaTable()
fgsea
20 days ago • updated 17 days ago Chris ▴ 10
3
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4
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298
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Store output of matchPWM()
biostrings Biostrings
20 days ago • updated 7 days ago mat149 ▴ 70
0
votes
4
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381
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 9 days ago by • 0 • written 20 days ago by ▴ 70
1
vote
2
replies
297
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
20 days ago • updated 19 days ago Yveto • 0
0
votes
3
replies
305
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 19 days ago by 42k • written 20 days ago by • 0
3
votes
4
replies
270
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Help with error using camera() in limma
CAMERA limma
21 days ago • updated 20 days ago Chris ▴ 10
1
vote
1
reply
161
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
0
votes
0
replies
96
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News: BioC2024 deadlines approaching
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21 days ago Maria Doyle ▴ 70
0
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1
reply
141
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putting my own expression data in deseq2
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updated 21 days ago by ★ 4.1k • written 21 days ago by • 0
0
votes
2
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173
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Timecourse RNASeq analysis
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21 days ago • updated 18 days ago Aurora • 0
0
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1
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128
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Version 3.15 S4Vectors packages are missing
S4Vectors
updated 21 days ago by 3.9k • written 21 days ago by • 0
0
votes
1
reply
267
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 21 days ago by 66k • written 21 days ago by • 0
0
votes
1
reply
141
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
1,749 results • Page 2 of 35
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Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
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Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
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The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
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We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
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After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
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how to control age and gender effect in expression data using DESeq2
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