3
votes
1
reply
147
views
How to save the DEXSeq results
DEXSeq
updated 11 days ago by 42k • written 11 days ago by • 0
4
votes
5
replies
313
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Method to find pathways different between 2 groups
fgsea GSVA CAMERA
11 days ago • updated 2 days ago Chris ▴ 10
0
votes
3
replies
220
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Couldn't connect to server while using "pathways"
graphite
updated 11 days ago by 42k • written 11 days ago by • 0
2
votes
1
reply
141
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 11 days ago by 42k • written 11 days ago by ▴ 70
1
vote
1
reply
184
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Handling multiple differential expression comparisons
DESeq2
updated 12 days ago by 42k • written 14 days ago by ▴ 10
2
votes
2
replies
223
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fgsea significant result
fgsea
12 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 3 days ago by 42k • written 15 months ago by • 0
0
votes
6
replies
285
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 13 days ago by ★ 1.4k • written 14 days ago by ▴ 130
1
vote
2
replies
396
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 13 days ago by 50k • written 13 days ago by • 0
2
votes
3
replies
261
views
package goseq seems to be not available on the latest version of R
goseq
updated 11 days ago by 50k • written 14 days ago by ▴ 20
2
votes
3
replies
252
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 12 days ago by ★ 4.1k • written 14 days ago by • 0
0
votes
0
replies
117
views
dba.plotProfile() plotting and interpretation
DiffBind
14 days ago Henry ▴ 10
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 14 days ago by 50k • written 15 days ago by • 0
0
votes
1
reply
154
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 14 days ago by 50k • written 15 days ago by • 0
4
votes
2
replies
619
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
15 days ago • updated 11 days ago gene_bioconductor ▴ 10
0
votes
0
replies
95
views
flowStats for CyTOF
flowStats
15 days ago tholmes • 0
0
votes
2
replies
159
views
DESeq2 v1.35.0
DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
0
votes
0
replies
88
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
15 days ago yvonneh • 0
0
votes
0
replies
83
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
15 days ago Ian D. ▴ 70
0
votes
1
reply
129
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 15 days ago by • 0
0
votes
4
replies
364
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 5 days ago by • 0 • written 16 days ago by ▴ 70
0
votes
2
replies
207
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
15 days ago • updated 14 days ago kcarey • 0
0
votes
3
replies
218
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 15 days ago by ★ 4.1k • written 15 days ago by • 0
1
vote
3
replies
302
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 9 days ago by ★ 4.1k • written 16 days ago by • 0
4
votes
0
replies
134
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
16 days ago shepherl 3.9k
0
votes
0
replies
134
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Empty table plot using plotGseaTable()
fgsea
16 days ago • updated 13 days ago Chris ▴ 10
0
votes
3
replies
300
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 15 days ago by 42k • written 16 days ago by • 0
1
vote
2
replies
285
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
16 days ago • updated 15 days ago Yveto • 0
0
votes
1
reply
261
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 17 days ago by 65k • written 17 days ago by • 0
3
votes
4
replies
259
views
Help with error using camera() in limma
CAMERA limma
17 days ago Chris ▴ 10
1
vote
1
reply
154
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 17 days ago by 42k • written 17 days ago by • 0
0
votes
2
replies
165
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
17 days ago • updated 14 days ago Aurora • 0
0
votes
1
reply
138
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 17 days ago by 42k • written 18 days ago by • 0
0
votes
0
replies
93
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
17 days ago Maria Doyle ▴ 70
0
votes
1
reply
122
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 17 days ago by 3.9k • written 17 days ago by • 0
0
votes
1
reply
134
views
putting my own expression data in deseq2
DESeq2
updated 17 days ago by ★ 4.1k • written 17 days ago by • 0
2
votes
2
replies
232
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
18 days ago Chris ▴ 10
0
votes
3
replies
273
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 17 days ago by 65k • written 18 days ago by • 0
0
votes
0
replies
94
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
18 days ago Chris ▴ 10
3
votes
3
replies
266
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 18 days ago by ★ 4.1k • written 18 days ago by ▴ 10
1
vote
1
reply
152
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 20 days ago by ▴ 40 • written 21 days ago by ★ 1.5k
0
votes
2
replies
225
views
PCA plot suggestions
DESeq2 PCAtools
updated 21 days ago by 42k • written 22 days ago by • 0
1
vote
3
replies
250
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 21 days ago by 42k • written 22 days ago by • 0
0
votes
1
reply
169
views
ATACseq merge peaks
DiffBind
updated 21 days ago by ★ 4.1k • written 23 days ago by • 0
1
vote
2
replies
211
views
Improving the design matrices vignette in RNAseq123
RNAseq123
25 days ago • updated 11 days ago Lluís Revilla Sancho ▴ 730
1
vote
7
replies
355
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
22 days ago • updated 21 days ago pl23 • 0
2
votes
9
replies
426
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 22 days ago by 65k • written 22 days ago by • 0
0
votes
0
replies
141
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
22 days ago • updated 14 days ago glaciya2018 • 0
1
vote
2
replies
175
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
23 days ago • updated 22 days ago ATpoint ★ 4.1k
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 22 days ago by 42k • written 23 days ago by • 0
192 results • Page 2 of 4
Recent ...
Replies
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…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters by anne-laure • 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
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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