1
vote
1
reply
184
views
Handling multiple differential expression comparisons
DESeq2
updated 11 days ago by 42k • written 13 days ago by ▴ 10
0
votes
0
replies
115
views
dba.plotProfile() plotting and interpretation
DiffBind
13 days ago Henry ▴ 10
0
votes
6
replies
281
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 12 days ago by ★ 1.4k • written 14 days ago by ▴ 130
4
votes
2
replies
617
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
14 days ago • updated 10 days ago gene_bioconductor ▴ 10
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 14 days ago by 50k • written 14 days ago by • 0
0
votes
1
reply
152
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 14 days ago by 50k • written 14 days ago by • 0
0
votes
0
replies
95
views
flowStats for CyTOF
flowStats
14 days ago tholmes • 0
0
votes
2
replies
157
views
DESeq2 v1.35.0
DESeq2
updated 14 days ago by 42k • written 14 days ago by • 0
0
votes
0
replies
88
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
14 days ago yvonneh • 0
0
votes
0
replies
81
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
14 days ago Ian D. ▴ 70
0
votes
1
reply
127
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 14 days ago by • 0
0
votes
2
replies
204
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
15 days ago • updated 14 days ago kcarey • 0
0
votes
3
replies
209
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 14 days ago by ★ 4.1k • written 15 days ago by • 0
1
vote
3
replies
300
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 8 days ago by ★ 4.1k • written 15 days ago by • 0
4
votes
0
replies
130
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
15 days ago shepherl 3.9k
0
votes
0
replies
133
views
Empty table plot using plotGseaTable()
fgsea
15 days ago • updated 13 days ago Chris ▴ 10
3
votes
4
replies
264
views
Store output of matchPWM()
biostrings Biostrings
15 days ago • updated 3 days ago mat149 ▴ 70
0
votes
4
replies
358
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 5 days ago by • 0 • written 15 days ago by ▴ 70
1
vote
2
replies
283
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
3
replies
298
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
3
votes
4
replies
259
views
Help with error using camera() in limma
CAMERA limma
16 days ago Chris ▴ 10
1
vote
1
reply
150
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 16 days ago by 42k • written 16 days ago by • 0
0
votes
0
replies
92
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
16 days ago Maria Doyle ▴ 70
0
votes
1
reply
134
views
putting my own expression data in deseq2
DESeq2
updated 16 days ago by ★ 4.1k • written 16 days ago by • 0
0
votes
2
replies
165
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
16 days ago • updated 13 days ago Aurora • 0
0
votes
1
reply
119
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 16 days ago by 3.9k • written 17 days ago by • 0
0
votes
1
reply
260
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 16 days ago by 65k • written 17 days ago by • 0
0
votes
1
reply
135
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 16 days ago by 42k • written 17 days ago by • 0
2
votes
2
replies
230
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
17 days ago Chris ▴ 10
0
votes
0
replies
92
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
17 days ago Chris ▴ 10
0
votes
3
replies
270
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 16 days ago by 65k • written 17 days ago by • 0
3
votes
3
replies
264
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 17 days ago by ★ 4.1k • written 18 days ago by ▴ 10
1
vote
1
reply
151
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 20 days ago by ▴ 40 • written 20 days ago by ★ 1.5k
1
vote
3
replies
250
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 20 days ago by 42k • written 21 days ago by • 0
1
vote
7
replies
355
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
21 days ago • updated 20 days ago pl23 • 0
2
votes
9
replies
423
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 21 days ago by 65k • written 21 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
21 days ago • updated 13 days ago glaciya2018 • 0
0
votes
2
replies
225
views
PCA plot suggestions
DESeq2 PCAtools
updated 20 days ago by 42k • written 22 days ago by • 0
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 22 days ago by • 0
0
votes
1
reply
167
views
ATACseq merge peaks
DiffBind
updated 20 days ago by ★ 4.1k • written 22 days ago by • 0
0
votes
0
replies
99
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
22 days ago • updated 17 days ago Sara • 0
0
votes
0
replies
97
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
22 days ago Dario Strbenac ★ 1.5k
1
vote
2
replies
173
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
22 days ago • updated 21 days ago ATpoint ★ 4.1k
1
vote
3
replies
234
views
Different Shrunk Log2FC according with reference
DESeq2
updated 22 days ago by 42k • written 22 days ago by ▴ 20
1
vote
4
replies
353
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
22 days ago • updated 20 days ago winwater0928 • 0
2
votes
5
replies
302
views
get BM error
ensembldb
updated 22 days ago by 65k • written 22 days ago by • 0
2
votes
5
replies
258
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 21 days ago by 65k • written 23 days ago by • 0
1
vote
2
replies
201
views
Citation for edgeR user guide
edgeR
written 23 days ago by ▴ 30
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 23 days ago by 42k • written 23 days ago by ▴ 40
1
vote
1
reply
131
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 23 days ago by 65k • written 23 days ago by ▴ 10
45,663 results • Page 2 of 914
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
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
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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