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79
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
10 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
206
views
Different Shrunk Log2FC according with reference
DESeq2
updated 10 days ago by
Michael Love
41k • written 10 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
313
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
10 days ago • updated 8 days ago
winwater0928
• 0
3
votes
1
reply
304
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 10 days ago by
Michael Love
41k • written 11 days ago by
i.sudbery
▴ 40
1
vote
1
reply
173
views
Citation for edgeR user guide
edgeR
updated 10 days ago by
Gordon Smyth
50k • written 11 days ago by
k___
▴ 30
0
votes
7
replies
692
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
9 weeks ago • updated 11 days ago
shepherl
3.9k
1
vote
1
reply
108
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 11 days ago by
James W. MacDonald
65k • written 11 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
340
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 9 days ago by
swbarnes2
★ 1.3k • written 11 days ago by
Aaliya
• 0
0
votes
0
replies
71
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
11 days ago
info
▴ 10
1
vote
4
replies
201
views
minfi::read.metharray.exp
minfiData
minfi
updated 10 days ago by
Basti
▴ 780 • written 12 days ago by
clacarion
• 0
0
votes
2
replies
242
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
11 days ago • updated 9 days ago
shuwangxinze1996
• 0
1
vote
2
replies
992
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 11 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
2
replies
155
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 11 days ago by
taur.vil
• 0
3
votes
3
replies
220
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 11 days ago by
Michael Love
41k • written 12 days ago by
WardDeb
• 0
1
vote
4
replies
230
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 12 days ago by
James W. MacDonald
65k • written 16 days ago by
Mirella Aurora
• 0
0
votes
1
reply
125
views
FDR via q-value
qvalue
updated 12 days ago by
James W. MacDonald
65k • written 15 days ago by
John
• 0
0
votes
5
replies
293
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 10 days ago by
James W. MacDonald
65k • written 13 days ago by
Gayatri
• 0
0
votes
2
replies
209
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
15 days ago • updated 12 days ago
catv
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 12 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 12 days ago
shepherl
3.9k
1
vote
13
replies
393
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
13 days ago • updated 10 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
81
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
13 days ago
vaxahey107
• 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
14 days ago • updated 3 days ago
Chris
• 0
0
votes
0
replies
93
views
I am trying to detect alternative splicing.
ASpli
14 days ago
Sebashish
• 0
3
votes
2
replies
212
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 12 days ago by
Guido Hooiveld
★ 3.9k • written 15 days ago by
fernanda.backsouza
▴ 10
0
votes
3
replies
147
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
bas_work
▴ 30
2
votes
2
replies
183
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
sansan
• 0
1
vote
0
replies
277
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
15 days ago
BioinfGuru
▴ 30
4
votes
6
replies
423
views
FilterByExpr low counts with small sample size
edgeR
17 days ago • updated 12 days ago
Jonathan
▴ 10
0
votes
2
replies
130
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
15 days ago
prity6459
• 0
0
votes
3
replies
182
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 15 days ago by
Gordon Smyth
50k • written 16 days ago by
prity6459
• 0
3
votes
1
reply
173
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 15 days ago by
Gordon Smyth
50k • written 16 days ago by
Shaimaa Gamal
• 0
0
votes
4
replies
193
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
16 days ago
sropri
• 0
0
votes
3
replies
158
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 4 days ago by
Alejandro Reyes
★ 1.9k • written 16 days ago by
Alessia
• 0
0
votes
1
reply
151
views
Adding columns to DEXSeqResults object
DEXSeq
updated 16 days ago by
Alejandro Reyes
★ 1.9k • written 18 days ago by
Clyde
• 0
0
votes
0
replies
118
views
Warning while loading DEP package
DEP
updated 16 days ago by
shepherl
3.9k • written 16 days ago by
Namrata
• 0
0
votes
1
reply
132
views
rlog transformation
DESeq2
updated 16 days ago by
Michael Love
41k • written 16 days ago by
ishij9717
• 0
0
votes
1
reply
111
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 16 days ago by
Michael Love
41k • written 16 days ago by
09191919
• 0
1
vote
2
replies
704
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
17 days ago • updated 8 days ago
ussarizona
▴ 10
0
votes
1
reply
130
views
covariate with negative and positive values
DESeq2
updated 16 days ago by
Michael Love
41k • written 17 days ago by
Brynn
• 0
0
votes
1
reply
145
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
quanah.hudson
• 0
1
vote
2
replies
210
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
16 days ago
Le
• 0
1
vote
2
replies
154
views
Error in champ.load(): The following specified files do not exist
ChAMP
17 days ago • updated 16 days ago
Sherin
• 0
0
votes
1
reply
98
views
Input Question for deseq.r
RSeqAn
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Nina
• 0
0
votes
4
replies
235
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
17 days ago • updated 14 days ago
lonn
• 0
0
votes
7
replies
311
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
17 days ago • updated 11 days ago
hortense96
• 0
0
votes
0
replies
76
views
News:
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Enzyme Engineering
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79
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News:
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flowBeads
17 days ago
bocsci11
• 0
0
votes
0
replies
92
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Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
18 days ago
Maliha Tabassum
• 0
199 results • Page
2 of 4
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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