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0
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0
replies
14
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
8 hours ago
JalapenoCornbread
• 0
0
votes
6
replies
86
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
updated 5 hours ago by
James W. MacDonald
65k • written 10 hours ago by
pl23
• 0
2
votes
9
replies
198
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 8 hours ago by
James W. MacDonald
65k • written 15 hours ago by
Alexandre
• 0
0
votes
0
replies
28
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
20 hours ago
glaciya2018
• 0
1
vote
2
replies
88
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
1 day ago • updated 20 hours ago
ATpoint
★ 4.0k
0
votes
1
reply
56
views
PCA plot suggestions
DESeq2
PCAtools
updated 14 hours ago by
JKim
• 0 • written 1 day ago by
Aaliya
• 0
0
votes
1
reply
75
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 1 day ago by
Michael Love
41k • written 1 day ago by
kcarey
• 0
0
votes
0
replies
23
views
ATACseq merge peaks
DiffBind
1 day ago
Shloka
• 0
0
votes
0
replies
20
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
1 day ago
Sara
• 0
2
votes
5
replies
147
views
get BM error
ensembldb
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
Fara
• 0
2
votes
5
replies
143
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 11 hours ago by
James W. MacDonald
65k • written 2 days ago by
bandconductor
• 0
0
votes
0
replies
29
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
1 day ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
100
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
1
vote
3
replies
129
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 15 hours ago by
James W. MacDonald
65k • written 1 day ago by
winwater0928
• 0
3
votes
1
reply
212
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
i.sudbery
▴ 40
1
vote
1
reply
81
views
Citation for edgeR user guide
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
k___
▴ 30
0
votes
7
replies
617
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
8 weeks ago • updated 2 days ago
shepherl
3.8k
1
vote
1
reply
62
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
234
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 22 hours ago by
swbarnes2
★ 1.3k • written 2 days ago by
Aaliya
• 0
0
votes
0
replies
27
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
2 days ago
info
▴ 10
1
vote
4
replies
137
views
minfi::read.metharray.exp
minfiData
minfi
updated 1 day ago by
Basti
▴ 780 • written 3 days ago by
clacarion
• 0
0
votes
2
replies
116
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
2 days ago • updated 22 hours ago
shuwangxinze1996
• 0
1
vote
2
replies
929
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 3 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
1
reply
93
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
taur.vil
• 0
3
votes
3
replies
168
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
WardDeb
• 0
1
vote
4
replies
156
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 3 days ago by
James W. MacDonald
65k • written 7 days ago by
Mirella Aurora
• 0
0
votes
1
reply
85
views
FDR via q-value
qvalue
updated 3 days ago by
James W. MacDonald
65k • written 6 days ago by
John
• 0
0
votes
5
replies
220
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 1 day ago by
James W. MacDonald
65k • written 4 days ago by
Gayatri
• 0
0
votes
2
replies
154
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
6 days ago • updated 3 days ago
catv
• 0
0
votes
0
replies
50
views
Improving the design matrices vignette in RNAseq123
RNAseq123
3 days ago
Lluís Revilla Sancho
▴ 730
0
votes
3
replies
1.1k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 4 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 3 days ago
shepherl
3.8k
1
vote
13
replies
274
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
4 days ago • updated 1 day ago
fernanda.backsouza
▴ 10
0
votes
0
replies
44
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
4 days ago
vaxahey107
• 0
12
votes
12
replies
774
views
Why p value inconsistent when using different number of pathway score?
limma
updated 4 days ago by
Robert Castelo
★ 3.3k • written 5 days ago by
Chris
• 0
0
votes
0
replies
63
views
I am trying to detect alternative splicing.
ASpli
5 days ago
Sebashish
• 0
3
votes
2
replies
164
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 6 days ago by
fernanda.backsouza
▴ 10
0
votes
3
replies
103
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
bas_work
▴ 30
2
votes
2
replies
140
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 6 days ago by
James W. MacDonald
65k • written 7 days ago by
sansan
• 0
1
vote
0
replies
205
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
6 days ago
BioinfGuru
▴ 30
4
votes
6
replies
334
views
FilterByExpr low counts with small sample size
edgeR
8 days ago • updated 3 days ago
Jonathan
▴ 10
0
votes
2
replies
91
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
6 days ago
prity6459
• 0
0
votes
3
replies
129
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
prity6459
• 0
3
votes
1
reply
120
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
Shaimaa Gamal
• 0
0
votes
4
replies
134
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
7 days ago
sropri
• 0
0
votes
1
reply
84
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 7 days ago by
Alejandro Reyes
★ 1.9k • written 7 days ago by
Alessia
• 0
0
votes
1
reply
119
views
Adding columns to DEXSeqResults object
DEXSeq
updated 7 days ago by
Alejandro Reyes
★ 1.9k • written 9 days ago by
Clyde
• 0
0
votes
0
replies
87
views
Warning while loading DEP package
DEP
updated 7 days ago by
shepherl
3.8k • written 7 days ago by
Namrata
• 0
0
votes
1
reply
90
views
rlog transformation
DESeq2
updated 7 days ago by
Michael Love
41k • written 7 days ago by
ishij9717
• 0
0
votes
1
reply
90
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 7 days ago by
Michael Love
41k • written 7 days ago by
09191919
• 0
45,580 results • Page
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Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Hi, Yes, I've tried this, but I am not sure if it is possible to assign `bquote` values to the names of a vector. In particular, if I use…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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