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464
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putting my own expression data in deseq2
DESeq2
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
Dev
• 0
2
votes
4
replies
2.1k
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
written 19 months ago by
Chris
▴ 20
0
votes
3
replies
920
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
SSSJec
• 0
0
votes
1
reply
1.2k
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
written 19 months ago by
Chris
▴ 20
3
votes
3
replies
1.1k
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
bioinf
▴ 10
1
vote
1
reply
637
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 19 months ago by
Leo Lahti
▴ 40 • written 19 months ago by
Dario Strbenac
★ 1.6k
0
votes
2
replies
746
views
PCA plot suggestions
DESeq2
PCAtools
updated 19 months ago by
Michael Love
43k • written 19 months ago by
Aaliya
• 0
1
vote
3
replies
1.1k
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 19 months ago by
Michael Love
43k • written 19 months ago by
JalapenoCornbread
• 0
0
votes
1
reply
1.3k
views
ATACseq merge peaks
DiffBind
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
Shloka
• 0
1
vote
2
replies
732
views
Improving the design matrices vignette in RNAseq123
RNAseq123
19 months ago
Lluís Revilla Sancho
▴ 760
1
vote
7
replies
1.2k
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
19 months ago
pl23
• 0
2
votes
9
replies
1.8k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Alexandre
• 0
0
votes
0
replies
745
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
19 months ago
glaciya2018
• 0
1
vote
2
replies
784
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
19 months ago
ATpoint
★ 5.0k
0
votes
1
reply
853
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 19 months ago by
Michael Love
43k • written 19 months ago by
kcarey
• 0
0
votes
0
replies
556
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
19 months ago
Sara
• 0
2
votes
5
replies
1.1k
views
get BM error
ensembldb
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Fara
• 0
2
votes
5
replies
1.0k
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
bandconductor
• 0
0
votes
0
replies
479
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
19 months ago
Dario Strbenac
★ 1.6k
1
vote
3
replies
761
views
Different Shrunk Log2FC according with reference
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
andrebolerbarros
▴ 20
1
vote
4
replies
1.1k
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
19 months ago
winwater0928
• 0
3
votes
1
reply
884
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
i.sudbery
▴ 40
1
vote
2
replies
1.6k
views
Citation for edgeR user guide
edgeR
written 19 months ago by
k___
▴ 30
1
vote
1
reply
755
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
fernanda.backsouza
▴ 30
0
votes
7
replies
2.7k
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 19 months ago by
swbarnes2
★ 1.4k • written 19 months ago by
Aaliya
• 0
0
votes
0
replies
589
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
19 months ago
info
▴ 10
1
vote
4
replies
933
views
minfi::read.metharray.exp
minfiData
minfi
updated 19 months ago by
Basti
▴ 780 • written 19 months ago by
clacarion
• 0
0
votes
2
replies
914
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
19 months ago
shuwangxinze1996
• 0
1
vote
2
replies
2.3k
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 19 months ago by
Tim Peters
▴ 230 • written 2.8 years ago by
jose.ramirez1
▴ 10
0
votes
2
replies
803
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 19 months ago by
taur.vil
• 0
3
votes
3
replies
1.1k
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
WardDeb
• 0
2
votes
4
replies
1.6k
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Mirella Aurora
• 0
0
votes
1
reply
559
views
FDR via q-value
qvalue
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
John
• 0
1
vote
8
replies
1.5k
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 14 months ago by
James W. MacDonald
68k • written 19 months ago by
Gayatri
• 0
0
votes
2
replies
1.2k
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
19 months ago
catv
• 0
0
votes
13
replies
3.5k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
written 3.1 years ago by
Maria Doyle
▴ 110
6
votes
12
replies
8.6k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
2.1 years ago • updated 19 months ago
shepherl
4.2k
5
votes
13
replies
4.1k
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
19 months ago
fernanda.backsouza
▴ 30
15
votes
17
replies
3.6k
views
Why p value inconsistent when using different number of pathway score?
limma
19 months ago
Chris
▴ 20
0
votes
0
replies
517
views
I am trying to detect alternative splicing.
ASpli
19 months ago
Sebashish
• 0
4
votes
2
replies
940
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 19 months ago by
Guido Hooiveld
★ 4.1k • written 19 months ago by
fernanda.backsouza
▴ 30
1
vote
3
replies
954
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
bas_work
▴ 30
2
votes
2
replies
1.6k
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
sansan
• 0
1
vote
0
replies
8.3k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
19 months ago
BioinfGuru
▴ 70
4
votes
6
replies
1.8k
views
FilterByExpr low counts with small sample size
edgeR
19 months ago
Jonathan
▴ 10
0
votes
2
replies
720
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
19 months ago
prity6459
• 0
0
votes
3
replies
983
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
prity6459
• 0
5
votes
3
replies
1.6k
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
Shaimaa Gamal
• 0
0
votes
8
replies
2.7k
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
updated 18 months ago by
alserg
▴ 280 • written 19 months ago by
sropri
• 0
0
votes
3
replies
881
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 19 months ago by
Alejandro Reyes
★ 1.9k • written 19 months ago by
Alessia
• 0
46,691 results • Page
25 of 934
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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