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2
replies
204
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WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
21 days ago • updated 16 days ago
w.cookson
• 0
0
votes
2
replies
140
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
16 days ago • updated 15 days ago
michelafrancesconi8
• 0
0
votes
1
reply
109
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 16 days ago by
James W. MacDonald
65k • written 16 days ago by
Reeya
• 0
0
votes
4
replies
211
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 16 days ago by
Michael Love
41k • written 17 days ago by
Aidan
• 0
0
votes
4
replies
384
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
17 days ago • updated 16 days ago
Lucy
▴ 60
0
votes
1
reply
90
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
Leyre
• 0
0
votes
2
replies
153
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
17 days ago
Seongsu
• 0
0
votes
2
replies
156
views
Gene Ontology doubt
microbiomeExplorer
18 days ago • updated 14 days ago
Bhawna
• 0
0
votes
1
reply
146
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 17 days ago by
Michael Love
41k • written 20 days ago by
saadmurtazakhan
▴ 10
0
votes
1
reply
126
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 16 days ago by
James W. MacDonald
65k • written 18 days ago by
ja569116
• 0
0
votes
2
replies
260
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
18 days ago • updated 13 days ago
fer_talavera
• 0
0
votes
1
reply
195
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
updated 10 days ago by
Wei Shi
★ 3.6k • written 18 days ago by
isaac.vock
• 0
0
votes
7
replies
316
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
19 days ago • updated 16 days ago
needNGS
• 0
14
votes
19
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
20 days ago • updated 11 days ago
Chris
• 0
3
votes
5
replies
324
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 19 days ago by
Gordon Smyth
50k • written 21 days ago by
Fabian
• 0
0
votes
2
replies
154
views
Minfi - estimatecellscount
min
minfi
20 days ago
clacarion
• 0
0
votes
0
replies
92
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
20 days ago
feather-W
• 0
0
votes
0
replies
90
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
20 days ago
Ankit
▴ 20
0
votes
6
replies
301
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 20 days ago by
Gordon Smyth
50k • written 21 days ago by
Faisal
• 0
1
vote
5
replies
285
views
fgsea fork
fgsea
updated 20 days ago by
James W. MacDonald
65k • written 21 days ago by
yimjohns
• 0
0
votes
1
reply
131
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 21 days ago by
Michael Love
41k • written 21 days ago by
Mikushi
• 0
0
votes
0
replies
78
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
21 days ago
Pierre Lindenbaum
▴ 10
2
votes
8
replies
472
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 22 days ago by
Gordon Smyth
50k • written 23 days ago by
Amit
• 0
0
votes
1
reply
107
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
Karen
• 0
2
votes
3
replies
309
views
PCA of different bacterial species
DESeq2
updated 22 days ago by
Michael Love
41k • written 23 days ago by
Laura
▴ 10
1
vote
2
replies
207
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
23 days ago
Mj.A.
• 0
0
votes
1
reply
226
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
6 weeks ago • updated 23 days ago
shepherl
3.8k
0
votes
2
replies
182
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 23 days ago by
Michael Love
41k • written 23 days ago by
SG
• 0
2
votes
3
replies
223
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 23 days ago by
Wei Shi
★ 3.6k • written 24 days ago by
thomas.heigl.ibk
• 0
2
votes
2
replies
190
views
From a DNAStringSet to a data.frame
Biostrings
24 days ago • updated 23 days ago
ramiro.barrantes
▴ 10
0
votes
1
reply
146
views
collapseReplicates dimension error
DESeq2
Dese
updated 24 days ago by
Michael Love
41k • written 27 days ago by
Léa
• 0
5
votes
25
replies
777
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 14 days ago by
Gordon Smyth
50k • written 24 days ago by
Jitendra
▴ 10
0
votes
2
replies
151
views
bioconductor emailing list
Bioconductor
updated 24 days ago by
shepherl
3.8k • written 24 days ago by
1427972815
• 0
3
votes
2
replies
188
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
24 days ago
Anita
▴ 10
3
votes
3
replies
330
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 24 days ago by
alan.ocallaghan
▴ 160 • written 25 days ago by
Najla Abassi
• 0
2
votes
1
reply
209
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 24 days ago by
ATpoint
★ 4.0k • written 25 days ago by
Dario Strbenac
★ 1.5k
0
votes
0
replies
97
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
24 days ago
gshweta95
• 0
0
votes
2
replies
303
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
27 days ago • updated 16 days ago
Gordon
• 0
7
votes
6
replies
409
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 27 days ago by
Gordon Smyth
50k • written 27 days ago by
Amit
• 0
2
votes
1
reply
175
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 25 days ago by
Guido Hooiveld
★ 3.9k • written 27 days ago by
enee
▴ 10
0
votes
0
replies
116
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
27 days ago
Maria Doyle
▴ 70
0
votes
0
replies
106
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
27 days ago
shepherl
3.8k
0
votes
1
reply
203
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 28 days ago by
Gordon Smyth
50k • written 28 days ago by
scoops_streams_06
• 0
0
votes
0
replies
99
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
28 days ago
nromerov
• 0
1
vote
2
replies
195
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
28 days ago • updated 22 days ago
Chanderkant Chaudhary
• 0
1
vote
3
replies
229
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 28 days ago by
Marcel Ramos
690 • written 28 days ago by
Astrid Deschênes
• 0
5
votes
3
replies
663
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 22 days ago by
Gordon Smyth
50k • written 29 days ago by
Jack S.
▴ 50
4
votes
4
replies
3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 29 days ago by
jandrade
• 0 • written 6.3 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
2
replies
195
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
29 days ago • updated 28 days ago
kcarey
• 0
0
votes
0
replies
107
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
29 days ago
mayra.haedo
• 0
199 results • Page
3 of 4
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Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
Le
• 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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