2
votes
3
replies
251
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 11 days ago by ★ 4.1k • written 13 days ago by • 0
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
116
views
dba.plotProfile() plotting and interpretation
DiffBind
13 days ago Henry ▴ 10
0
votes
6
replies
282
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
4
votes
2
replies
618
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
82
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
129
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 14 days ago by • 0
0
votes
2
replies
206
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
15 days ago • updated 14 days ago kcarey • 0
0
votes
3
replies
213
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
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 15 days ago by • 0
4
votes
0
replies
133
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
265
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
299
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
17 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
136
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
231
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
271
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
265
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
425
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
22 days ago • updated 14 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
168
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 18 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 ATpoint ★ 4.1k
1
vote
3
replies
234
views
Different Shrunk Log2FC according with reference
DESeq2
updated 22 days ago by 42k • written 23 days ago by ▴ 20
1
vote
4
replies
353
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
23 days ago • updated 21 days ago winwater0928 • 0
2
votes
5
replies
302
views
get BM error
ensembldb
updated 22 days ago by 65k • written 23 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
194 results • Page 2 of 4
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Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
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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…
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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
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