2
votes
7
replies
424
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
13 days ago • updated 10 days ago sajadahmad41454 • 0
0
votes
0
replies
78
views
Treeio as.treedata function seq lenght error
treeio
13 days ago nromerov • 0
2
votes
2
replies
287
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
13 days ago • updated 8 days ago zzrammal • 0
3
votes
10
replies
493
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 10 days ago by 66k • written 13 days ago by • 0
0
votes
1
reply
122
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 14 days ago by 3.9k • written 14 days ago by • 0
2
votes
1
reply
188
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 13 days ago by 66k • written 14 days ago by • 0
0
votes
0
replies
100
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
14 days ago Dinesh • 0
3
votes
5
replies
307
views
Help with running egsea()
EGSEA
14 days ago • updated 13 days ago Chris ▴ 10
3
votes
1
reply
156
views
How to save the DEXSeq results
DEXSeq
updated 14 days ago by 42k • written 14 days ago by • 0
2
votes
1
reply
150
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 14 days ago by 42k • written 14 days ago by ▴ 70
0
votes
3
replies
236
views
Couldn't connect to server while using "pathways"
graphite
updated 14 days ago by 42k • written 15 days ago by • 0
4
votes
5
replies
343
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
15 days ago • updated 5 days ago Chris ▴ 10
7
votes
6
replies
642
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 15 days ago by • 0
2
votes
2
replies
236
views
fgsea significant result
fgsea
16 days ago • updated 15 days ago Chris ▴ 10
1
vote
2
replies
409
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 17 days ago by 50k • written 17 days ago by • 0
2
votes
3
replies
279
views
package goseq seems to be not available on the latest version of R
goseq
updated 15 days ago by 50k • written 17 days ago by ▴ 20
2
votes
3
replies
263
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 16 days ago by ★ 4.1k • written 17 days ago by • 0
1
vote
1
reply
195
views
Handling multiple differential expression comparisons
DESeq2
updated 16 days ago by 42k • written 17 days ago by ▴ 10
0
votes
0
replies
125
views
dba.plotProfile() plotting and interpretation
DiffBind
17 days ago Henry ▴ 10
0
votes
6
replies
306
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 17 days ago by ★ 1.4k • written 18 days ago by ▴ 130
4
votes
2
replies
641
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
18 days ago • updated 14 days ago gene_bioconductor ▴ 10
0
votes
1
reply
180
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 18 days ago by 50k • written 18 days ago by • 0
0
votes
1
reply
164
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 18 days ago by 50k • written 18 days ago by • 0
0
votes
0
replies
100
views
flowStats for CyTOF
flowStats
18 days ago tholmes • 0
0
votes
2
replies
175
views
DESeq2 v1.35.0
DESeq2
updated 18 days ago by 42k • written 18 days ago by • 0
0
votes
0
replies
97
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
18 days ago yvonneh • 0
0
votes
0
replies
89
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
18 days ago Ian D. ▴ 70
0
votes
1
reply
145
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 19 days ago by • 0
0
votes
2
replies
217
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
19 days ago • updated 18 days ago kcarey • 0
0
votes
3
replies
230
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 days ago by ★ 4.1k • written 19 days ago by • 0
1
vote
3
replies
306
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 13 days ago by ★ 4.1k • written 19 days ago by • 0
4
votes
0
replies
147
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
19 days ago shepherl 3.9k
0
votes
0
replies
142
views
Empty table plot using plotGseaTable()
fgsea
19 days ago • updated 17 days ago Chris ▴ 10
3
votes
4
replies
296
views
Store output of matchPWM()
biostrings Biostrings
19 days ago • updated 7 days ago mat149 ▴ 70
0
votes
4
replies
379
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 9 days ago by • 0 • written 20 days ago by ▴ 70
1
vote
2
replies
295
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
20 days ago • updated 19 days ago Yveto • 0
0
votes
3
replies
305
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 19 days ago by 42k • written 20 days ago by • 0
3
votes
4
replies
268
views
Help with error using camera() in limma
CAMERA limma
20 days ago Chris ▴ 10
1
vote
1
reply
161
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
0
votes
0
replies
96
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
20 days ago Maria Doyle ▴ 70
0
votes
1
reply
141
views
putting my own expression data in deseq2
DESeq2
updated 21 days ago by ★ 4.1k • written 21 days ago by • 0
0
votes
2
replies
172
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
21 days ago • updated 18 days ago Aurora • 0
0
votes
1
reply
126
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 20 days ago by 3.9k • written 21 days ago by • 0
0
votes
1
reply
267
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 20 days ago by 66k • written 21 days ago by • 0
0
votes
1
reply
140
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
2
votes
2
replies
240
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
21 days ago Chris ▴ 10
0
votes
0
replies
98
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
21 days ago Chris ▴ 10
0
votes
3
replies
283
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 20 days ago by 66k • written 21 days ago by • 0
3
votes
3
replies
275
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 22 days ago by ★ 4.1k • written 22 days ago by ▴ 10
1
vote
1
reply
155
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 24 days ago by ▴ 40 • written 25 days ago by ★ 1.5k
170 results • Page 2 of 4
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt by blackwidowzzz • 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Votes
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
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