1
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1
reply
201
views
Handling multiple differential expression comparisons
DESeq2
updated 22 days ago by 42k • written 24 days ago by ▴ 10
2
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2
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253
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fgsea significant result
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22 days ago Chris ▴ 10
0
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44
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3.2k
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How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 13 days ago by 42k • written 15 months ago by • 0
0
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6
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323
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 23 days ago by ★ 1.4k • written 25 days ago by ▴ 130
1
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2
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421
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 23 days ago by 50k • written 24 days ago by • 0
2
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3
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320
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package goseq seems to be not available on the latest version of R
goseq
updated 21 days ago by 50k • written 24 days ago by ▴ 20
2
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3
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279
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 22 days ago by ★ 4.2k • written 24 days ago by • 0
0
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0
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132
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dba.plotProfile() plotting and interpretation
DiffBind
24 days ago Henry ▴ 10
0
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1
reply
187
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 24 days ago by 50k • written 25 days ago by • 0
0
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1
reply
172
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Gene-by-sample covariates in limma
Metabolomics limma
updated 24 days ago by 50k • written 25 days ago by • 0
4
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2
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660
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
25 days ago • updated 21 days ago gene_bioconductor ▴ 10
0
votes
0
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106
views
flowStats for CyTOF
flowStats
25 days ago tholmes • 0
0
votes
2
replies
188
views
DESeq2 v1.35.0
DESeq2
updated 25 days ago by 42k • written 25 days ago by • 0
0
votes
0
replies
104
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
25 days ago yvonneh • 0
0
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0
replies
97
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
25 days ago Ian D. ▴ 70
0
votes
1
reply
158
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 25 days ago by • 0
0
votes
5
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426
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
26 days ago • updated 3 days ago Ian D. ▴ 70
0
votes
2
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224
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Deseq2 and Normalization of RNA sequencing data
DESeq2
26 days ago • updated 24 days ago kcarey • 0
0
votes
3
replies
248
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 25 days ago by ★ 4.2k • written 26 days ago by • 0
1
vote
3
replies
329
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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 19 days ago by ★ 4.2k • written 26 days ago by • 0
4
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0
replies
165
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News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
26 days ago shepherl 3.9k
0
votes
0
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148
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Empty table plot using plotGseaTable()
fgsea
26 days ago • updated 24 days ago Chris ▴ 10
0
votes
3
replies
312
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 26 days ago by 42k • written 27 days ago by • 0
1
vote
2
replies
325
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
26 days ago • updated 25 days ago Yveto • 0
0
votes
1
reply
272
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 27 days ago by 66k • written 27 days ago by • 0
3
votes
4
replies
280
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Help with error using camera() in limma
CAMERA limma
27 days ago Chris ▴ 10
1
vote
1
reply
166
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 27 days ago by 42k • written 27 days ago by • 0
0
votes
2
replies
184
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
27 days ago • updated 24 days ago Aurora • 0
0
votes
1
reply
144
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 27 days ago by 42k • written 28 days ago by • 0
0
votes
0
replies
101
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News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
27 days ago Maria Doyle ▴ 70
0
votes
1
reply
135
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 27 days ago by 3.9k • written 27 days ago by • 0
0
votes
1
reply
143
views
putting my own expression data in deseq2
DESeq2
updated 27 days ago by ★ 4.2k • written 27 days ago by • 0
2
votes
2
replies
251
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
28 days ago Chris ▴ 10
0
votes
3
replies
286
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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 27 days ago by 66k • written 28 days ago by • 0
0
votes
0
replies
103
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
28 days ago Chris ▴ 10
3
votes
3
replies
282
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 28 days ago by ★ 4.2k • written 28 days ago by ▴ 10
1
vote
1
reply
166
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 4 weeks ago by ▴ 40 • written 4 weeks ago by ★ 1.5k
0
votes
2
replies
241
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PCA plot suggestions
DESeq2 PCAtools
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
1
vote
3
replies
266
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
votes
1
reply
190
views
ATACseq merge peaks
DiffBind
updated 4 weeks ago by ★ 4.2k • written 4 weeks ago by • 0
1
vote
2
replies
228
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Improving the design matrices vignette in RNAseq123
RNAseq123
5 weeks ago • updated 21 days ago Lluís Revilla Sancho ▴ 730
1
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7
replies
388
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Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
4 weeks ago pl23 • 0
2
votes
9
replies
462
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 4 weeks ago by 66k • written 4 weeks ago by • 0
0
votes
0
replies
154
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
4 weeks ago • updated 24 days ago glaciya2018 • 0
1
vote
2
replies
188
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
4 weeks ago ATpoint ★ 4.2k
0
votes
1
reply
177
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
votes
0
replies
108
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
4 weeks ago • updated 28 days ago Sara • 0
2
votes
5
replies
339
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get BM error
ensembldb
updated 4 weeks ago by 66k • written 4 weeks ago by • 0
2
votes
5
replies
286
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 4 weeks ago by 66k • written 4 weeks ago by • 0
0
votes
0
replies
102
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
4 weeks ago Dario Strbenac ★ 1.5k
1,000 results • Page 3 of 20
Recent ...
Replies
Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by ATpoint ★ 4.2k
I don't have an answer to the "why" but maybe a simple reimplemention will do: ```r seqs <- c("ATCATCGTATCAAAGTC", "AAAACGTATCAAAGTC", "TG…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Guido Hooiveld ★ 4.0k
After checking `?DESeqDataSetFromMatrix` note this information: arguments provided to SummarizedExperiment including rowRanges and met…
Answer: Error in gseDO function by Guido Hooiveld ★ 4.0k
Yes, you are missing something. :-) For a GSEA you will need to use as input all genes that you are analyzing; these genes should be ran…
Comment: GSVA function by Robert Castelo ★ 3.3k
No, negative values may occur after log transformation when the `log(x)` is taken from a positive number `x with 0 < x < 1`, and therefore …
Comment: conumee with Infinium MethylationEPIC v2.0 by sgomez • 0
Hi Max, Could you try this? https://support.bioconductor.org/p/9136138/#9136840
Votes
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
A: DiffBind Batch Effect
A: DiffBind Batch Effect
C: DiffBind Batch Effect
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