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0
votes
0
replies
97
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
21 days ago
yvonneh
• 0
0
votes
0
replies
90
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
21 days ago
Ian D.
▴ 70
0
votes
1
reply
150
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 22 days ago by
4r-rtg
• 0
0
votes
4
replies
388
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 12 days ago by
Ziliang
• 0 • written 23 days ago by
Ian D.
▴ 70
0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
22 days ago • updated 21 days ago
kcarey
• 0
0
votes
3
replies
240
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 22 days ago by
ATpoint
★ 4.2k • written 22 days ago by
james.zhang20
• 0
1
vote
3
replies
321
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 16 days ago by
ATpoint
★ 4.2k • written 22 days ago by
angelathuynh5
• 0
4
votes
0
replies
149
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
22 days ago
shepherl
3.9k
0
votes
0
replies
143
views
Empty table plot using plotGseaTable()
fgsea
22 days ago • updated 20 days ago
Chris
▴ 10
0
votes
3
replies
310
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 22 days ago by
Michael Love
42k • written 23 days ago by
HAK
• 0
1
vote
2
replies
313
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
23 days ago • updated 22 days ago
Yveto
• 0
0
votes
1
reply
270
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 23 days ago by
James W. MacDonald
66k • written 24 days ago by
SSSJec
• 0
3
votes
4
replies
280
views
Help with error using camera() in limma
CAMERA
limma
23 days ago
Chris
▴ 10
1
vote
1
reply
162
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
marcusn
• 0
0
votes
2
replies
179
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
24 days ago • updated 21 days ago
Aurora
• 0
0
votes
1
reply
144
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 23 days ago by
Michael Love
42k • written 24 days ago by
Agung
• 0
0
votes
0
replies
99
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
23 days ago
Maria Doyle
▴ 70
0
votes
1
reply
133
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 23 days ago by
shepherl
3.9k • written 24 days ago by
bounlu
• 0
0
votes
1
reply
143
views
putting my own expression data in deseq2
DESeq2
updated 24 days ago by
ATpoint
★ 4.2k • written 24 days ago by
Dev
• 0
2
votes
2
replies
248
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
24 days ago
Chris
▴ 10
0
votes
3
replies
286
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 23 days ago by
James W. MacDonald
66k • written 24 days ago by
SSSJec
• 0
0
votes
0
replies
100
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
24 days ago
Chris
▴ 10
3
votes
3
replies
279
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 25 days ago by
ATpoint
★ 4.2k • written 25 days ago by
bioinf
▴ 10
1
vote
1
reply
160
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 27 days ago by
Leo Lahti
▴ 40 • written 27 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
233
views
PCA plot suggestions
DESeq2
PCAtools
updated 27 days ago by
Michael Love
42k • written 29 days ago by
Aaliya
• 0
1
vote
3
replies
261
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 27 days ago by
Michael Love
42k • written 28 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
184
views
ATACseq merge peaks
DiffBind
updated 27 days ago by
ATpoint
★ 4.2k • written 29 days ago by
Shloka
• 0
1
vote
2
replies
222
views
Improving the design matrices vignette in RNAseq123
RNAseq123
4 weeks ago • updated 17 days ago
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
377
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
28 days ago • updated 27 days ago
pl23
• 0
2
votes
9
replies
449
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 28 days ago by
James W. MacDonald
66k • written 28 days ago by
Alexandre
• 0
0
votes
0
replies
149
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
29 days ago • updated 21 days ago
glaciya2018
• 0
1
vote
2
replies
182
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
4 weeks ago • updated 29 days ago
ATpoint
★ 4.2k
0
votes
1
reply
170
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 29 days ago by
Michael Love
42k • written 29 days ago by
kcarey
• 0
0
votes
0
replies
102
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
29 days ago • updated 25 days ago
Sara
• 0
2
votes
5
replies
330
views
get BM error
ensembldb
updated 29 days ago by
James W. MacDonald
66k • written 4 weeks ago by
Fara
• 0
2
votes
5
replies
279
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 28 days ago by
James W. MacDonald
66k • written 4 weeks ago by
bandconductor
• 0
0
votes
0
replies
99
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
29 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
245
views
Different Shrunk Log2FC according with reference
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
andrebolerbarros
▴ 20
1
vote
4
replies
366
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
4 weeks ago • updated 28 days ago
winwater0928
• 0
1
vote
2
replies
222
views
Citation for edgeR user guide
edgeR
written 4 weeks ago by
k___
▴ 30
0
votes
8
replies
412
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 29 days ago by
swbarnes2
★ 1.4k • written 4 weeks ago by
Aaliya
• 0
0
votes
2
replies
279
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
4 weeks ago • updated 29 days ago
shuwangxinze1996
• 0
0
votes
2
replies
201
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 4 weeks ago by
taur.vil
• 0
0
votes
5
replies
341
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 29 days ago by
James W. MacDonald
66k • written 4 weeks ago by
Gayatri
• 0
0
votes
4
replies
1.3k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 7 days ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
2
votes
13
replies
540
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
4 weeks ago • updated 29 days ago
fernanda.backsouza
▴ 10
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 22 days ago
Chris
▴ 10
5
votes
3
replies
329
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 14 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Shaimaa Gamal
• 0
0
votes
3
replies
197
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 23 days ago by
Alejandro Reyes
★ 1.9k • written 5 weeks ago by
Alessia
• 0
1
vote
2
replies
772
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
5 weeks ago • updated 27 days ago
Patadù
▴ 10
182 results • Page
3 of 4
Recent ...
Replies
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
Wei Shi
★ 3.6k
Your bam file names should be stored in a vector and then provided to the `files` parameter.
Comment: Volcano plot of scRNA-seq data not "centered"
by
Michael Love
42k
Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…
Answer: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
ATpoint
★ 4.2k
I was talking about the command line version.
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
I tried reading in the .csv version of the SAF with header = F and I'm still getting an error. I'm running: ``` counts <- featureCounts( …
Votes
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
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★ 4.2k
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