0
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0
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88
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Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
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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
DESeq2 rnaseqGene Normalization
updated 12 days ago by ★ 4.1k • written 12 days ago by • 0
1
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2
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289
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
12 days ago • updated 11 days ago Dylan.Sheerin • 0
2
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7
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424
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deseq2 results
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13 days ago • updated 10 days ago sajadahmad41454 • 0
0
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0
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78
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Treeio as.treedata function seq lenght error
treeio
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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13 days ago • updated 8 days ago zzrammal • 0
3
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10
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493
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 11 days ago by 66k • written 14 days ago by • 0
0
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1
reply
122
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Recovering my account credentials on Bioconductor
Bioconductor
updated 14 days ago by 3.9k • written 14 days ago by • 0
2
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1
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190
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minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 14 days ago by 66k • written 14 days ago by • 0
0
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0
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100
views
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()
EGSEA
14 days ago • updated 13 days ago Chris ▴ 10
3
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1
reply
156
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How to save the DEXSeq results
DEXSeq
updated 15 days ago by 42k • written 15 days ago by • 0
2
votes
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
votes
3
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236
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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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343
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Method to find pathways different between 2 groups
fgsea GSVA CAMERA
15 days ago • updated 6 days ago Chris ▴ 10
7
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6
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643
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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
replies
237
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fgsea significant result
fgsea
16 days ago • updated 15 days ago Chris ▴ 10
1
vote
2
replies
409
views
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
replies
282
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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
votes
3
replies
264
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 16 days ago by ★ 4.1k • written 17 days ago by • 0
1
vote
1
reply
195
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Handling multiple differential expression comparisons
DESeq2
updated 16 days ago by 42k • written 17 days ago by ▴ 10
0
votes
0
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125
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dba.plotProfile() plotting and interpretation
DiffBind
17 days ago Henry ▴ 10
0
votes
6
replies
307
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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
votes
2
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642
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
18 days ago • updated 14 days ago gene_bioconductor ▴ 10
0
votes
1
reply
181
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 18 days ago by 50k • written 18 days ago by • 0
0
votes
1
reply
165
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Gene-by-sample covariates in limma
Metabolomics limma
updated 18 days ago by 50k • written 18 days ago by • 0
0
votes
0
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100
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flowStats for CyTOF
flowStats
18 days ago tholmes • 0
0
votes
2
replies
175
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DESeq2 v1.35.0
DESeq2
updated 18 days ago by 42k • written 18 days ago by • 0
0
votes
0
replies
97
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
18 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?
DiffBind
19 days ago Ian D. ▴ 70
0
votes
1
reply
145
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 19 days ago by • 0
0
votes
2
replies
217
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Deseq2 and Normalization of RNA sequencing data
DESeq2
19 days ago • updated 18 days ago kcarey • 0
0
votes
3
replies
230
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 days ago by ★ 4.1k • written 19 days ago by • 0
1
vote
3
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307
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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
votes
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
19 days ago • updated 17 days ago Chris ▴ 10
3
votes
4
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296
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Store output of matchPWM()
biostrings Biostrings
19 days ago • updated 7 days ago mat149 ▴ 70
0
votes
4
replies
380
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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
296
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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
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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
BioC2024 Bioconductor Community
21 days ago Maria Doyle ▴ 70
0
votes
1
reply
141
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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
172
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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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127
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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 20 days ago by 66k • written 21 days ago by • 0
0
votes
1
reply
140
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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
2
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2
replies
240
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
21 days ago Chris ▴ 10
0
votes
0
replies
98
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
22 days ago • updated 21 days ago Chris ▴ 10
1,000 results • Page 2 of 20
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Comment: ChAMP installation issue by Tahirah • 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by James W. MacDonald 66k
Yes, you can use `limma`.
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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