2
votes
2
replies
418
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
10 days ago • updated 5 days ago Matthew Thornton ▴ 360
0
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1
reply
189
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
0
votes
0
replies
89
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer ShinyApps
12 days ago neilzhao ▴ 30
0
votes
1
reply
116
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 12 days ago by ★ 4.1k • written 12 days ago by • 0
1
vote
2
replies
291
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
13 days ago • updated 12 days ago Dylan.Sheerin • 0
2
votes
7
replies
432
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
13 days ago • updated 10 days ago sajadahmad41454 • 0
0
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0
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79
views
Treeio as.treedata function seq lenght error
treeio
14 days ago nromerov • 0
2
votes
2
replies
289
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
14 days ago • updated 8 days ago zzrammal • 0
3
votes
10
replies
496
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 11 days ago by 66k • written 14 days ago by • 0
0
votes
1
reply
122
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 14 days ago by 3.9k • written 14 days ago by • 0
2
votes
1
reply
192
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 14 days ago by 66k • written 14 days ago by • 0
0
votes
0
replies
102
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
15 days ago Dinesh • 0
3
votes
5
replies
310
views
Help with running egsea()
EGSEA
15 days ago • updated 13 days ago Chris ▴ 10
3
votes
1
reply
158
views
How to save the DEXSeq results
DEXSeq
updated 15 days ago by 42k • written 15 days ago by • 0
2
votes
1
reply
150
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 15 days ago by 42k • written 15 days ago by ▴ 70
0
votes
3
replies
238
views
Couldn't connect to server while using "pathways"
graphite
updated 15 days ago by 42k • written 15 days ago by • 0
4
votes
5
replies
345
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
16 days ago • updated 6 days ago Chris ▴ 10
7
votes
6
replies
647
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 16 days ago by • 0
2
votes
2
replies
240
views
fgsea significant result
fgsea
17 days ago • updated 16 days ago Chris ▴ 10
1
vote
2
replies
410
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 18 days ago by 50k • written 18 days ago by • 0
2
votes
3
replies
288
views
package goseq seems to be not available on the latest version of R
goseq
updated 15 days ago by 50k • written 18 days ago by ▴ 20
2
votes
3
replies
265
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 16 days ago by ★ 4.1k • written 18 days ago by • 0
1
vote
1
reply
196
views
Handling multiple differential expression comparisons
DESeq2
updated 16 days ago by 42k • written 18 days ago by ▴ 10
0
votes
0
replies
125
views
dba.plotProfile() plotting and interpretation
DiffBind
18 days ago Henry ▴ 10
0
votes
6
replies
309
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 17 days ago by ★ 1.4k • written 19 days ago by ▴ 130
4
votes
2
replies
643
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
19 days ago • updated 15 days ago gene_bioconductor ▴ 10
0
votes
1
reply
181
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 19 days ago by 50k • written 19 days ago by • 0
0
votes
1
reply
166
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Gene-by-sample covariates in limma
Metabolomics limma
updated 19 days ago by 50k • written 19 days ago by • 0
0
votes
0
replies
100
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flowStats for CyTOF
flowStats
19 days ago tholmes • 0
0
votes
2
replies
175
views
DESeq2 v1.35.0
DESeq2
updated 19 days ago by 42k • written 19 days ago by • 0
0
votes
0
replies
97
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
19 days ago yvonneh • 0
0
votes
0
replies
89
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
19 days ago Ian D. ▴ 70
0
votes
1
reply
146
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 19 days ago by • 0
0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
20 days ago • updated 19 days ago kcarey • 0
0
votes
3
replies
231
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 days ago by ★ 4.1k • written 20 days ago by • 0
1
vote
3
replies
311
views
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 20 days ago by • 0
4
votes
0
replies
147
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
20 days ago shepherl 3.9k
0
votes
0
replies
143
views
Empty table plot using plotGseaTable()
fgsea
20 days ago • updated 18 days ago Chris ▴ 10
3
votes
4
replies
299
views
Store output of matchPWM()
biostrings Biostrings
20 days ago • updated 8 days ago mat149 ▴ 70
0
votes
4
replies
381
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 10 days ago by • 0 • written 20 days ago by ▴ 70
1
vote
2
replies
301
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
21 days ago • updated 20 days ago Yveto • 0
0
votes
3
replies
307
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
3
votes
4
replies
273
views
Help with error using camera() in limma
CAMERA limma
21 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
97
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
21 days ago Maria Doyle ▴ 70
0
votes
1
reply
141
views
putting my own expression data in deseq2
DESeq2
updated 21 days ago by ★ 4.1k • written 21 days ago by • 0
0
votes
2
replies
174
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
21 days ago • updated 18 days ago Aurora • 0
0
votes
1
reply
128
views
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
268
views
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 22 days ago by • 0
0
votes
1
reply
142
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 21 days ago by 42k • written 22 days ago by • 0
178 results • Page 2 of 4
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Thank you so much!
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…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
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 …
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
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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Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
how to control age and gender effect in expression data using DESeq2
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