0
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0
replies
13
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
3 hours ago Dinesh • 0
3
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4
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83
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Help with running egsea()
EGSEA
6 hours ago • updated 4 hours ago Chris • 0
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News: Nominations for Bioconductor Awards 2024!
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6 weeks ago • updated 7 hours ago shepherl 3.9k
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1
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41
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How to save the DEXSeq results
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updated 10 hours ago by 41k • written 11 hours ago by • 0
3
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3
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Method to find pathways different between 2 groups
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updated 10 hours ago by ★ 3.3k • written 1 day ago by • 0
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3
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80
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Couldn't connect to server while using "pathways"
graphite
updated 6 hours ago by 41k • written 19 hours ago by • 0
1
vote
1
reply
55
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 11 hours ago by 41k • written 12 hours ago by ▴ 70
1
vote
3
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84
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
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updated 2 hours ago by 16k • written 1 day ago by • 0
1
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1
reply
99
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Handling multiple differential expression comparisons
DESeq2
updated 1 day ago by 41k • written 3 days ago by ▴ 10
2
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2
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124
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fgsea significant result
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2 days ago • updated 1 day ago Chris • 0
0
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34
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How to use bootRanges to bootstrap small RNA loci (nullranges package)
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15 months ago • updated 4 hours ago Poonam • 0
0
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6
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214
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Once again a "Model matrix not full rank"
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updated 2 days ago by ★ 1.3k • written 4 days ago by ▴ 130
1
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2
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332
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 3 days ago by 50k • written 3 days ago by • 0
2
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3
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156
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package goseq seems to be not available on the latest version of R
goseq
updated 14 hours ago by 50k • written 3 days ago by ▴ 20
2
votes
3
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174
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Too many significant genes when integrating gtex and tcga
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updated 1 day ago by ★ 4.1k • written 3 days ago by • 0
0
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0
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53
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dba.plotProfile() plotting and interpretation
DiffBind
3 days ago Henry ▴ 10
0
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1
reply
109
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 4 days ago by 50k • written 4 days ago by • 0
0
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1
reply
101
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Gene-by-sample covariates in limma
Metabolomics limma
updated 4 days ago by 50k • written 4 days ago by • 0
4
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2
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531
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
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4 days ago • updated 8 hours ago gene_bioconductor ▴ 10
0
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0
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50
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flowStats for CyTOF
flowStats
4 days ago tholmes • 0
0
votes
2
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107
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DESeq2 v1.35.0
DESeq2
updated 4 days ago by 41k • written 4 days ago by • 0
0
votes
0
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48
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
4 days ago yvonneh • 0
0
votes
0
replies
44
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
4 days ago Ian D. ▴ 70
0
votes
1
reply
68
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 4 days ago by • 0
0
votes
2
replies
131
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
5 days ago • updated 4 days ago Ian D. ▴ 70
0
votes
2
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137
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Deseq2 and Normalization of RNA sequencing data
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5 days ago • updated 4 days ago kcarey • 0
0
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3
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Differences in differential analysis methods for RNA-Seq
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updated 4 days ago by ★ 4.1k • written 5 days ago by • 0
0
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1
reply
142
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
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updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
3
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0
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73
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News: Bioconductor 3.19 is Released!
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5 days ago shepherl 3.9k
0
votes
0
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90
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Empty table plot using plotGseaTable()
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5 days ago • updated 3 days ago Chris • 0
0
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3
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156
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Store output of matchPWM()
biostrings Biostrings
updated 5 days ago by 65k • written 5 days ago by ▴ 70
0
votes
3
replies
252
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
1
vote
2
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229
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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6 days ago • updated 5 days ago Yveto • 0
8
votes
7
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1.7k
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 17 hours ago by • 0 • written 6.7 years ago by ▴ 80
0
votes
1
reply
228
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 6 days ago by 65k • written 6 days ago by • 0
3
votes
4
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210
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Help with error using camera() in limma
CAMERA limma
6 days ago Chris • 0
1
vote
1
reply
109
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 6 days ago by 41k • written 6 days ago by • 0
0
votes
2
replies
123
views
Timecourse RNASeq analysis
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6 days ago • updated 3 days ago Aurora • 0
0
votes
1
reply
103
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
0
votes
0
replies
63
views
News: BioC2024 deadlines approaching
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6 days ago Maria Doyle ▴ 70
0
votes
1
reply
88
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 6 days ago by 3.9k • written 6 days ago by • 0
0
votes
1
reply
110
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putting my own expression data in deseq2
DESeq2
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
2
votes
2
replies
195
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
7 days ago Chris • 0
0
votes
3
replies
242
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 6 days ago by 65k • written 7 days ago by • 0
0
votes
0
replies
75
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
7 days ago Chris • 0
3
votes
3
replies
235
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 7 days ago by ★ 4.1k • written 7 days ago by ▴ 10
1
vote
1
reply
130
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 10 days ago by ▴ 40 • written 10 days ago by ★ 1.5k
0
votes
2
replies
210
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PCA plot suggestions
DESeq2 PCAtools
updated 10 days ago by 41k • written 11 days ago by • 0
1
vote
3
replies
222
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 10 days ago by 41k • written 11 days ago by • 0
0
votes
1
reply
138
views
ATACseq merge peaks
DiffBind
updated 10 days ago by ★ 4.1k • written 12 days ago by • 0
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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