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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
just now
Ian D.
▴ 70
0
votes
1
reply
24
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 4 hours ago by
4r-rtg
• 0
0
votes
2
replies
66
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated just now
Ian D.
▴ 70
0
votes
1
reply
39
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
updated 5 hours ago by
ATpoint
★ 4.1k • written 16 hours ago by
kcarey
• 0
0
votes
3
replies
78
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 4 hours ago by
ATpoint
★ 4.1k • written 16 hours ago by
james.zhang20
• 0
0
votes
1
reply
90
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 18 hours ago by
ATpoint
★ 4.1k • written 18 hours ago by
angelathuynh5
• 0
2
votes
0
replies
33
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
18 hours ago
shepherl
3.8k
0
votes
0
replies
51
views
Empty table plot using plotGseaTable()
fgsea
20 hours ago • updated 18 hours ago
Chris
• 0
0
votes
3
replies
102
views
Store output of matchPWM()
biostrings
Biostrings
updated 20 hours ago by
James W. MacDonald
65k • written 23 hours ago by
mat149
▴ 70
0
votes
3
replies
208
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 17 hours ago by
Michael Love
41k • written 1 day ago by
HAK
• 0
0
votes
2
replies
183
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
1 day ago • updated 13 hours ago
Yveto
• 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 1 day ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
201
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
SSSJec
• 0
3
votes
4
replies
163
views
Help with error using camera() in limma
CAMERA
limma
1 day ago
Chris
• 0
1
vote
1
reply
76
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
marcusn
• 0
0
votes
1
reply
71
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Aurora
• 0
0
votes
1
reply
83
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Agung
• 0
0
votes
0
replies
42
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
2 days ago
Maria Doyle
▴ 70
0
votes
1
reply
59
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 2 days ago by
shepherl
3.8k • written 2 days ago by
bounlu
• 0
0
votes
1
reply
80
views
putting my own expression data in deseq2
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
Dev
• 0
2
votes
2
replies
165
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
2 days ago
Chris
• 0
0
votes
3
replies
202
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 1 day ago by
James W. MacDonald
65k • written 3 days ago by
SSSJec
• 0
0
votes
0
replies
51
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
3 days ago • updated 2 days ago
Chris
• 0
3
votes
3
replies
193
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
bioinf
▴ 10
1
vote
1
reply
106
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 5 days ago by
Leo Lahti
▴ 40 • written 6 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
180
views
PCA plot suggestions
DESeq2
PCAtools
updated 5 days ago by
Michael Love
41k • written 7 days ago by
Aaliya
• 0
1
vote
3
replies
185
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 6 days ago by
Michael Love
41k • written 6 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
111
views
ATACseq merge peaks
DiffBind
updated 6 days ago by
ATpoint
★ 4.1k • written 7 days ago by
Shloka
• 0
1
vote
1
reply
149
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 6 days ago by
Gordon Smyth
50k • written 10 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
287
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
6 days ago • updated 5 days ago
pl23
• 0
2
votes
9
replies
340
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 6 days ago by
James W. MacDonald
65k • written 7 days ago by
Alexandre
• 0
0
votes
0
replies
77
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
7 days ago
glaciya2018
• 0
1
vote
2
replies
139
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
8 days ago • updated 7 days ago
ATpoint
★ 4.1k
0
votes
1
reply
129
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 7 days ago by
Michael Love
41k • written 7 days ago by
kcarey
• 0
0
votes
0
replies
69
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
8 days ago • updated 3 days ago
Sara
• 0
2
votes
5
replies
236
views
get BM error
ensembldb
updated 7 days ago by
James W. MacDonald
65k • written 8 days ago by
Fara
• 0
2
votes
5
replies
213
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 6 days ago by
James W. MacDonald
65k • written 8 days ago by
bandconductor
• 0
0
votes
0
replies
72
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
8 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
200
views
Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by
Michael Love
41k • written 8 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
298
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago
winwater0928
• 0
3
votes
1
reply
293
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by
Michael Love
41k • written 8 days ago by
i.sudbery
▴ 40
1
vote
1
reply
158
views
Citation for edgeR user guide
edgeR
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
k___
▴ 30
0
votes
7
replies
682
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
8 weeks ago • updated 8 days ago
shepherl
3.8k
1
vote
1
reply
102
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
321
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 7 days ago by
swbarnes2
★ 1.3k • written 8 days ago by
Aaliya
• 0
0
votes
0
replies
63
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
9 days ago
info
▴ 10
1
vote
4
replies
192
views
minfi::read.metharray.exp
minfiData
minfi
updated 8 days ago by
Basti
▴ 780 • written 9 days ago by
clacarion
• 0
0
votes
2
replies
236
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
9 days ago • updated 7 days ago
shuwangxinze1996
• 0
1
vote
2
replies
979
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 9 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
2
replies
147
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 9 days ago by
taur.vil
• 0
200 results • Page
1 of 4
Recent ...
Replies
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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