3
votes
5
replies
291
views
Help with running egsea()
EGSEA
12 days ago • updated 10 days ago Chris ▴ 10
3
votes
1
reply
148
views
How to save the DEXSeq results
DEXSeq
updated 12 days ago by 42k • written 12 days ago by • 0
4
votes
5
replies
319
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
12 days ago • updated 3 days ago Chris ▴ 10
0
votes
3
replies
223
views
Couldn't connect to server while using "pathways"
graphite
updated 12 days ago by 42k • written 12 days ago by • 0
2
votes
1
reply
142
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 12 days ago by 42k • written 12 days ago by ▴ 70
1
vote
1
reply
189
views
Handling multiple differential expression comparisons
DESeq2
updated 13 days ago by 42k • written 15 days ago by ▴ 10
2
votes
2
replies
226
views
fgsea significant result
fgsea
14 days ago • updated 13 days ago Chris ▴ 10
0
votes
44
replies
3.1k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 4 days ago by 42k • written 15 months ago by • 0
0
votes
6
replies
293
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 14 days ago by ★ 1.4k • written 16 days ago by ▴ 130
1
vote
2
replies
403
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 14 days ago by 50k • written 15 days ago by • 0
2
votes
3
replies
267
views
package goseq seems to be not available on the latest version of R
goseq
updated 12 days ago by 50k • written 15 days ago by ▴ 20
2
votes
3
replies
254
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 13 days ago by ★ 4.1k • written 15 days ago by • 0
0
votes
0
replies
118
views
dba.plotProfile() plotting and interpretation
DiffBind
15 days ago Henry ▴ 10
0
votes
1
reply
175
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 16 days ago by 50k • written 16 days ago by • 0
0
votes
1
reply
155
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 16 days ago by 50k • written 16 days ago by • 0
4
votes
2
replies
624
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
16 days ago • updated 12 days ago gene_bioconductor ▴ 10
0
votes
0
replies
98
views
flowStats for CyTOF
flowStats
16 days ago tholmes • 0
0
votes
2
replies
162
views
DESeq2 v1.35.0
DESeq2
updated 16 days ago by 42k • written 16 days ago by • 0
0
votes
0
replies
91
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
16 days ago yvonneh • 0
0
votes
0
replies
87
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
16 days ago Ian D. ▴ 70
0
votes
1
reply
133
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 16 days ago by • 0
0
votes
4
replies
373
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 7 days ago by • 0 • written 17 days ago by ▴ 70
0
votes
2
replies
211
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
17 days ago • updated 16 days ago kcarey • 0
0
votes
3
replies
223
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 16 days ago by ★ 4.1k • written 17 days ago by • 0
1
vote
3
replies
304
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 10 days ago by ★ 4.1k • written 17 days ago by • 0
4
votes
0
replies
142
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
17 days ago shepherl 3.9k
0
votes
0
replies
138
views
Empty table plot using plotGseaTable()
fgsea
17 days ago • updated 15 days ago Chris ▴ 10
0
votes
3
replies
302
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 17 days ago by 42k • written 18 days ago by • 0
1
vote
2
replies
289
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
17 days ago • updated 16 days ago Yveto • 0
0
votes
1
reply
262
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 18 days ago by 65k • written 18 days ago by • 0
3
votes
4
replies
261
views
Help with error using camera() in limma
CAMERA limma
18 days ago Chris ▴ 10
1
vote
1
reply
156
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 18 days ago by 42k • written 18 days ago by • 0
0
votes
2
replies
169
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
18 days ago • updated 15 days ago Aurora • 0
0
votes
1
reply
139
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 18 days ago by 42k • written 19 days ago by • 0
0
votes
0
replies
94
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
18 days ago Maria Doyle ▴ 70
0
votes
1
reply
122
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 18 days ago by 3.9k • written 18 days ago by • 0
0
votes
1
reply
137
views
putting my own expression data in deseq2
DESeq2
updated 18 days ago by ★ 4.1k • written 18 days ago by • 0
2
votes
2
replies
235
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
19 days ago Chris ▴ 10
0
votes
3
replies
274
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 18 days ago by 65k • written 19 days ago by • 0
0
votes
0
replies
95
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
19 days ago Chris ▴ 10
3
votes
3
replies
269
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 19 days ago by ★ 4.1k • written 19 days ago by ▴ 10
1
vote
1
reply
153
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 22 days ago by ▴ 40 • written 22 days ago by ★ 1.5k
0
votes
2
replies
227
views
PCA plot suggestions
DESeq2 PCAtools
updated 22 days ago by 42k • written 23 days ago by • 0
1
vote
3
replies
253
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 22 days ago by 42k • written 23 days ago by • 0
0
votes
1
reply
171
views
ATACseq merge peaks
DiffBind
updated 22 days ago by ★ 4.1k • written 24 days ago by • 0
1
vote
2
replies
214
views
Improving the design matrices vignette in RNAseq123
RNAseq123
26 days ago • updated 12 days ago Lluís Revilla Sancho ▴ 730
1
vote
7
replies
359
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
23 days ago • updated 22 days ago pl23 • 0
2
votes
9
replies
427
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 23 days ago by 65k • written 23 days ago by • 0
0
votes
0
replies
143
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
23 days ago • updated 15 days ago glaciya2018 • 0
1
vote
2
replies
176
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
24 days ago • updated 23 days ago ATpoint ★ 4.1k
45,668 results • Page 2 of 914
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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