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25
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
written 2 hours ago by
kcarey
• 0
0
votes
0
replies
14
views
ATACseq merge peaks
DiffBind
2 hours ago
Shloka
• 0
0
votes
0
replies
11
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
4 hours ago
Sara
• 0
2
votes
5
replies
112
views
get BM error
ensembldb
updated 3 hours ago by
James W. MacDonald
65k • written 13 hours ago by
Fara
• 0
0
votes
3
replies
81
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 6 hours ago by
James W. MacDonald
65k • written 22 hours ago by
bandconductor
• 0
0
votes
0
replies
17
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
6 hours ago
Dario Strbenac
★ 1.5k
1
vote
0
replies
29
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
9 hours ago
ATpoint
★ 4.0k
1
vote
3
replies
69
views
Different Shrunk Log2FC according with reference
DESeq2
updated 7 hours ago by
Michael Love
41k • written 11 hours ago by
andrebolerbarros
▴ 20
0
votes
1
reply
44
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 2 hours ago by
swbarnes2
★ 1.3k • written 11 hours ago by
winwater0928
• 0
2
votes
1
reply
144
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 17 hours ago by
Michael Love
41k • written 1 day ago by
i.sudbery
▴ 40
1
vote
1
reply
55
views
Citation for edgeR user guide
edgeR
updated 21 hours ago by
Gordon Smyth
50k • written 1 day ago by
k___
▴ 30
0
votes
7
replies
608
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 1 day ago
shepherl
3.8k
1
vote
1
reply
51
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
fernanda.backsouza
▴ 10
0
votes
4
replies
108
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 2 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
Aaliya
• 0
0
votes
0
replies
21
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
1 day ago
info
▴ 10
1
vote
4
replies
125
views
minfi::read.metharray.exp
minfiData
minfi
updated 12 hours ago by
Basti
▴ 780 • written 2 days ago by
clacarion
• 0
0
votes
1
reply
57
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
updated 11 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
shuwangxinze1996
• 0
1
vote
2
replies
919
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 1 day ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
1
reply
82
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
taur.vil
• 0
3
votes
3
replies
143
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
WardDeb
• 0
1
vote
4
replies
138
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 2 days ago by
James W. MacDonald
65k • written 6 days ago by
Mirella Aurora
• 0
0
votes
1
reply
75
views
FDR via q-value
qvalue
updated 2 days ago by
James W. MacDonald
65k • written 5 days ago by
John
• 0
0
votes
5
replies
197
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 5 hours ago by
James W. MacDonald
65k • written 3 days ago by
Gayatri
• 0
0
votes
2
replies
147
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
5 days ago • updated 2 days ago
catv
• 0
0
votes
0
replies
40
views
Improving the design matrices vignette in RNAseq123
RNAseq123
2 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 2 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 2 days ago
shepherl
3.8k
1
vote
12
replies
214
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
updated 10 hours ago by
Guido Hooiveld
★ 3.9k • written 3 days ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
39
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
3 days ago
vaxahey107
• 0
12
votes
12
replies
746
views
Why p value inconsistent when using different number of pathway score?
limma
updated 2 days ago by
Robert Castelo
★ 3.3k • written 4 days ago by
Chris
• 0
0
votes
0
replies
59
views
I am trying to detect alternative splicing.
ASpli
4 days ago
Sebashish
• 0
3
votes
2
replies
148
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 2 days ago by
Guido Hooiveld
★ 3.9k • written 4 days ago by
fernanda.backsouza
▴ 10
0
votes
3
replies
98
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 5 days ago by
James W. MacDonald
65k • written 5 days ago by
bas_work
▴ 30
2
votes
2
replies
136
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 5 days ago by
James W. MacDonald
65k • written 5 days ago by
sansan
• 0
1
vote
0
replies
195
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
5 days ago
BioinfGuru
▴ 30
3
votes
6
replies
320
views
FilterByExpr low counts with small sample size
edgeR
7 days ago • updated 2 days ago
Jonathan
▴ 10
0
votes
2
replies
87
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
5 days ago
prity6459
• 0
0
votes
3
replies
125
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
prity6459
• 0
0
votes
1
reply
107
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Shaimaa Gamal
• 0
0
votes
4
replies
129
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
6 days ago • updated 5 days ago
sropri
• 0
0
votes
1
reply
78
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 days ago by
Alejandro Reyes
★ 1.9k • written 6 days ago by
Alessia
• 0
0
votes
1
reply
115
views
Adding columns to DEXSeqResults object
DEXSeq
updated 6 days ago by
Alejandro Reyes
★ 1.9k • written 8 days ago by
Clyde
• 0
0
votes
0
replies
85
views
Warning while loading DEP package
DEP
updated 6 days ago by
shepherl
3.8k • written 6 days ago by
Namrata
• 0
0
votes
1
reply
87
views
rlog transformation
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
ishij9717
• 0
0
votes
1
reply
85
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 6 days ago by
Michael Love
41k • written 6 days ago by
09191919
• 0
0
votes
1
reply
94
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
ussarizona
• 0
0
votes
1
reply
108
views
covariate with negative and positive values
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
Brynn
• 0
0
votes
1
reply
111
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 6 days ago by
ATpoint
★ 4.0k • written 7 days ago by
quanah.hudson
• 0
1
vote
2
replies
179
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
6 days ago • updated 5 days ago
Le
• 0
1
vote
2
replies
124
views
Error in champ.load(): The following specified files do not exist
ChAMP
6 days ago
Sherin
• 0
45,575 results • Page
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Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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