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4
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365
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
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updated 18 days ago by 65k • written 7 weeks ago by • 0
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EGSEA usage with microarray data (with vooma)?
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updated 8 days ago by ▴ 10 • written 7.4 years ago by ▴ 190
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Differential peaks that were not identified in diffbind were identified in diseq2
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Problem installing ChAMP on a MacBook
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log2FoldChange value is way too different when compared with counts(dds)
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updated 16 days ago by 42k • written 16 days ago by • 0
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How to correctly adjust for gender in edgeR
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ChipQC 'names' attribute [9] must be the same length as the vector [2]'
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
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A ComBat-seq issue: the covariates are confounded
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2
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3
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package goseq seems to be not available on the latest version of R
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SingleR Label.Ont
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3
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Reading huge bismark coverage files using bbseq::read.bismark
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3
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STRINGdb : error with string_db$plot_network()
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0
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Differences in differential analysis methods for RNA-Seq
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updated 15 days ago by ★ 4.1k • written 15 days ago by • 0
3
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3
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permutation test in edgeR
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updated 26 days ago by 50k • written 5 weeks ago by • 0
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3
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223
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
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Error retrieving ensembl gene id using biomaRt...
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3
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Log-cpm values from limma
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updated 7 days ago by 50k • written 29 days ago by • 0
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3
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888
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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updated 23 days ago by ★ 1.2k • written 14 months ago by ▴ 10
2
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3
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252
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Too many significant genes when integrating gtex and tcga
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updated 12 days ago by ★ 4.1k • written 14 days ago by • 0
1
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3
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Deseq2. decontXcounts not integers. Useful alternative?
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updated 21 days ago by 42k • written 22 days ago by • 0
1
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3
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0
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3
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273
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
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3
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Assymetric MA plot with no overall trend
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2
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2
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fgsea significant result
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12 days ago Chris ▴ 10
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2
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1 day ago makala • 0
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2
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limma for gene expression analysis with big and unbalanced sample size
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updated 17 days ago by • 0 • written 8.0 years ago by • 0
1
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2
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175
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Reproducibility issue with scran together with lapply and BiocParallel
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23 days ago • updated 22 days ago ATpoint ★ 4.1k
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2
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Timecourse RNASeq analysis
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17 days ago • updated 14 days ago Aurora • 0
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2
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Erroe when using makeOrgPackageFromNCBI()
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2 days ago Patadù ▴ 10
2
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2
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331
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Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
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5 days ago • updated 1 day ago Matthew Thornton ▴ 360
1
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2
replies
287
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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16 days ago • updated 15 days ago Yveto • 0
1
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2
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
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4 weeks ago • updated 21 days ago Patadù ▴ 10
0
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2
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159
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DESeq2 v1.35.0
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updated 15 days ago by 42k • written 15 days ago by • 0
2
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2
replies
211
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OrgDb for maize
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updated 28 days ago by 65k • written 29 days ago by • 0
1
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2
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Improving the design matrices vignette in RNAseq123
RNAseq123
25 days ago • updated 11 days ago Lluís Revilla Sancho ▴ 730
0
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2
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207
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Deseq2 and Normalization of RNA sequencing data
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15 days ago • updated 14 days ago kcarey • 0
4
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2
replies
619
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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
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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