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Votes
1
vote
4
replies
207
views
minfi::read.metharray.exp
minfiData
minfi
updated 12 days ago by
Basti
▴ 780 • written 14 days ago by
clacarion
• 0
0
votes
2
replies
130
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
5 days ago • updated 4 days ago
Ian D.
▴ 70
2
votes
3
replies
164
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 2 days ago by
Reza
• 0
0
votes
1
reply
134
views
covariate with negative and positive values
DESeq2
updated 18 days ago by
Michael Love
41k • written 19 days ago by
Brynn
• 0
3
votes
1
reply
315
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 12 days ago by
Michael Love
41k • written 13 days ago by
i.sudbery
▴ 40
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 18 days ago by
Michael Love
41k • written 18 days ago by
09191919
• 0
0
votes
1
reply
28
views
How to save the DEXSeq results
DEXSeq
updated 3 hours ago by
Michael Love
41k • written 3 hours ago by
Sara
• 0
4
votes
2
replies
502
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
3 days ago • updated 31 minutes ago
gene_bioconductor
▴ 10
1
vote
2
replies
527
views
GSVA error
GSVA
22 days ago • updated 21 days ago
Alex
• 0
1
vote
1
reply
129
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 9 days ago by
Leo Lahti
▴ 40 • written 10 days ago by
Dario Strbenac
★ 1.5k
4
votes
6
replies
431
views
FilterByExpr low counts with small sample size
edgeR
19 days ago • updated 14 days ago
Jonathan
▴ 10
0
votes
2
replies
61
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 5 hours ago by
Vincent J. Carey, Jr.
6.7k • written 21 hours ago by
robersy
• 0
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 17 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
126
views
FDR via q-value
qvalue
updated 14 days ago by
James W. MacDonald
65k • written 17 days ago by
John
• 0
3
votes
3
replies
228
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 13 days ago by
Michael Love
41k • written 14 days ago by
WardDeb
• 0
1
vote
2
replies
713
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
19 days ago • updated 10 days ago
ussarizona
▴ 10
0
votes
3
replies
206
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 20 days ago by
Michael Love
41k • written 21 days ago by
andrebolerbarros
▴ 20
0
votes
2
replies
222
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 26 days ago by
Michael Love
41k • written 4 weeks ago by
nhaus
▴ 30
0
votes
1
reply
165
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 26 days ago by
Michael Love
41k • written 27 days ago by
Adelaide
• 0
1
vote
2
replies
158
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
12 days ago • updated 11 days ago
ATpoint
★ 4.1k
0
votes
5
replies
302
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 12 days ago by
James W. MacDonald
65k • written 14 days ago by
Gayatri
• 0
0
votes
1
reply
156
views
Adding columns to DEXSeqResults object
DEXSeq
updated 18 days ago by
Alejandro Reyes
★ 1.9k • written 19 days ago by
Clyde
• 0
0
votes
3
replies
71
views
Couldn't connect to server while using "pathways"
DESeq2
updated 3 hours ago by
James W. MacDonald
65k • written 11 hours ago by
fduguchunhui
• 0
0
votes
3
replies
192
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 17 days ago by
Gordon Smyth
50k • written 18 days ago by
prity6459
• 0
0
votes
2
replies
226
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
5 days ago • updated 4 days ago
Yveto
• 0
0
votes
1
reply
137
views
rlog transformation
DESeq2
updated 18 days ago by
Michael Love
41k • written 18 days ago by
ishij9717
• 0
0
votes
2
replies
919
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
1
vote
2
replies
244
views
How to retrieve detailed regression results from deseq2
DESeq2
25 days ago • updated 16 days ago
Weiqian
▴ 10
2
votes
5
replies
240
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 11 days ago by
James W. MacDonald
65k • written 12 days ago by
bandconductor
• 0
0
votes
1
reply
108
views
putting my own expression data in deseq2
DESeq2
updated 6 days ago by
ATpoint
★ 4.1k • written 6 days ago by
Dev
• 0
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 11 days ago by
Michael Love
41k • written 12 days ago by
kcarey
• 0
0
votes
2
replies
122
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
6 days ago • updated 3 days ago
Aurora
• 0
3
votes
3
replies
233
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
bioinf
▴ 10
1
vote
3
replies
219
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 10 days ago by
Michael Love
41k • written 10 days ago by
JalapenoCornbread
• 0
0
votes
4
replies
245
views
Minfi - estimatecellscount
min
minfi
updated 7 days ago by
James W. MacDonald
65k • written 5 weeks ago by
clacarion
• 0
0
votes
7
replies
423
views
DESeq filtering specific to contrasts
DESeq2
updated 17 days ago by
Michael Love
41k • written 11 weeks ago by
Emma
• 0
0
votes
1
reply
144
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 20 days ago by
kamryncole1963
• 0 • written 25 days ago by
Sara
• 0
0
votes
1
reply
88
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 6 days ago by
shepherl
3.9k • written 6 days ago by
bounlu
• 0
0
votes
1
reply
151
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
zh9118
• 0
0
votes
2
replies
248
views
Regressing out batch effects
DESeq2
updated 26 days ago by
Michael Love
41k • written 4 weeks ago by
kys91240
• 0
0
votes
4
replies
203
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
17 days ago
sropri
• 0
0
votes
1
reply
707
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 23 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
1
reply
228
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 5 days ago by
James W. MacDonald
65k • written 6 days ago by
SSSJec
• 0
2
votes
2
replies
389
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
24 days ago
Henry
▴ 10
2
votes
3
replies
328
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
21 days ago • updated 20 days ago
daniel.carbajo
• 0
2
votes
2
replies
195
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
6 days ago
Chris
• 0
1
vote
1
reply
111
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
139
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 20 days ago by
James W. MacDonald
65k • written 22 days ago by
tian.liu0720
• 0
2
votes
2
replies
117
views
fgsea significant result
fgsea
1 day ago • updated 23 hours ago
Chris
• 0
1
vote
2
replies
301
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
4 weeks ago • updated 2 days ago
Kim
• 0
193 results • Page
2 of 4
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Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
gene_bioconductor
▴ 10
Thanks for your thoughtful and detailed comment, Gordon
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Answer: How to save the DEXSeq results
by
Michael Love
41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups
by
Robert Castelo
★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways"
by
James W. MacDonald
65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Votes
Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
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