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0
votes
0
replies
832
views
Improving Gene Matching for CIBERSORT Deconvolution with Monaco Reference Matrix in Bulk RNA-Seq
DeconRNASeq
AnnotationDbi
org.Hs.eg.db
19 months ago
chunglee13
• 0
0
votes
4
replies
2.0k
views
Trouble Installing DADA2 (warning: R new user)
dada2
updated 19 months ago by
shepherl
4.3k • written 19 months ago by
schott01
• 0
0
votes
0
replies
864
views
Difference in Predictive component of PLS and OPLS Model
Metabolomics
plotGrouper
Bioconductor
ropls
PLSDAbatch
19 months ago
devarti.mahakalkar
• 0
0
votes
0
replies
784
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi
EPICv2manifest
MethylAid
19 months ago
pcibin
• 0
0
votes
4
replies
9.5k
views
Any tools to convert .gff to .gtf format
AnnotationData
CrispRdesignR
BSgenome
updated 13 months ago by
ControlF5
• 0 • written 3.4 years ago by
Manoj Kumar R
• 0
0
votes
3
replies
1.0k
views
Conumee with EPICv2 Segment function
Conu
conumee
updated 10 months ago by
zpingfeng
• 0 • written 19 months ago by
idatta1
• 0
0
votes
0
replies
920
views
Job:
Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics
scRNAseq
19 months ago
Damini
• 0
0
votes
1
reply
750
views
single excel file containing methylation beta values does not get loaded in ChAMP
ChAMP
updated 19 months ago by
Basti
▴ 780 • written 19 months ago by
tahirah.yasmin2014
• 0
1
vote
2
replies
828
views
How to get the DMR?
ENmix
19 months ago
Alex
• 0
0
votes
0
replies
426
views
Remove Control Probes from Affymetrix Human Gene 1.0 ST Array probeset version
AffymetrixDataTestFiles
AffymetrixChip
19 months ago
drexjaramel
• 0
0
votes
3
replies
1.1k
views
How to search Pubmed Central or other fulltext literature base using regex?
metaMSdata
Bioconductor
19 months ago
Abiologist
• 0
0
votes
1
reply
4.5k
views
converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5
SingleCellExperiment
BPCells
SingleCellExper
updated 19 months ago by
yxsee
• 0 • written 19 months ago by
Le
• 0
0
votes
0
replies
532
views
Understanding Differentially Abundant Neighbourhood Identification
miloR
19 months ago
Dario Strbenac
★ 1.6k
2
votes
2
replies
5.6k
views
Unable to install the package "tissuesGeneExpression"
bioconductor
updated 19 months ago by
Muhammad Abdullah
• 0 • written 8.5 years ago by
mdroog
▴ 10
1
vote
13
replies
2.7k
views
Ranking the GSEA Results
fgsea
log2FC
19 months ago • updated 18 months ago
V_Vibes
• 0
1
vote
8
replies
2.1k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2
glmGamPoi
offset
edgeR
scRNAseq
updated 18 months ago by
Gordon Smyth
53k • written 19 months ago by
Alec
• 0
0
votes
2
replies
1.3k
views
Species level information couldn't find with DADA2 bioconductor package
Metagenomics
dada2
MicrobiomeData
19 months ago • updated 17 months ago
abhisek001
• 0
3
votes
1
reply
2.4k
views
Difference between enrichGO results and Enrichr website results
Pathways
GO.db
clusterProfiler
updated 19 months ago by
Guido Hooiveld
★ 4.1k • written 19 months ago by
adrip
▴ 10
0
votes
1
reply
600
views
Risa package missing from Bioconductor 3.19
3.19
Risa
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
rkjulian
• 0
1
vote
2
replies
1.2k
views
Struggling to convert a large list of non-model genes into human orthologs, any suggestions?
annotation
19 months ago
ronin
• 0
0
votes
0
replies
794
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution
rnaseqGene
RNAseq
19 months ago
JG13
• 0
0
votes
1
reply
825
views
BiomaRt listAttributes - which are external ?
Bioconductor
getBM
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Abiologist
• 0
0
votes
0
replies
860
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
19 months ago
gamma.jian
▴ 10
1
vote
2
replies
3.5k
views
Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
19 months ago
sropri
• 0
0
votes
5
replies
1.2k
views
modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 19 months ago by
Peter Hickey
▴ 760 • written 19 months ago by
Lluís Revilla Sancho
▴ 760
1
vote
4
replies
2.6k
views
SeSAMe DMR for EPIC V2
sesame
EPICv2manifest
epicv2
updated 6 months ago by
MargaretJDinan
• 0 • written 19 months ago by
luca.s
▴ 50
1
vote
5
replies
2.3k
views
EnsDb: bad_weak_ptr
AnnotationHub
BiocFileCache
19 months ago
Lluís Revilla Sancho
▴ 760
0
votes
5
replies
2.3k
views
Cannot connect to annotationhub server
AnnotationHub
ExperimentHub
updated 19 months ago by
shepherl
4.3k • written 19 months ago by
Mishaal Irfan
• 0
4
votes
4
replies
1.8k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma
adjustment
voom
removeBatchEffect
covariates
19 months ago
sukeshinik5
▴ 20
0
votes
0
replies
498
views
Structural Variant Format Converted for BRASS Format
StructuralVariantAnnotation
19 months ago
Dario Strbenac
★ 1.6k
0
votes
1
reply
619
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Neha
• 0
1
vote
2
replies
1.6k
views
Issues with retrieving mouse SNP dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
19 months ago
Svitlana
▴ 10
0
votes
0
replies
509
views
Differential Gene Wrapper for Propotion of Detected
scran
19 months ago
Dario Strbenac
★ 1.6k
0
votes
2
replies
1.8k
views
PCA (Principal Component Analysis) plots from ChIP-seq data
ChIPseqR
19 months ago
egbastakis
• 0
4
votes
4
replies
1.2k
views
Warning message when running limma with covariates
limma
19 months ago • updated 13 months ago
Chris
▴ 20
0
votes
9
replies
1.6k
views
Research Project - Expanding search funtionality on the GEO database
GEOquery
GEO
19 months ago
gallantk5
• 0
3
votes
5
replies
3.9k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 19 months ago by
Reza Ghamsari
• 0 • written 23 months ago by
Jack S.
▴ 60
0
votes
8
replies
2.3k
views
limma comparison for small sample size and how to get covariance matrix
covariancematrix
limma
19 months ago • updated 18 months ago
jiachengd
• 0
5
votes
5
replies
1.9k
views
Limma with covariates
limma
written 19 months ago by
Chris
▴ 20
1
vote
1
reply
837
views
DESeq2 - vst() - log2FC - no replicates
DESeq2
log2FC
vst()
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
lifeonmars
• 0
0
votes
2
replies
1.3k
views
Epicv2 conversion fail
minfi
19 months ago
Alex
• 0
1
vote
5
replies
1.2k
views
DESeq2 ML Query
DESeq2
updated 18 months ago by
Michael Love
43k • written 19 months ago by
chris2.a.white
• 0
1
vote
3
replies
1.1k
views
Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression
DESeq2
19 months ago • updated 17 months ago
David W. H.
• 0
0
votes
0
replies
876
views
Job:
Postdoc+PhD position: AI large-language models of single-cell data for cancer immunogenomics
JobPosting
AI
HPC
CuratedAtlasQueryR
19 months ago
Stefano Mangiola
▴ 40
0
votes
0
replies
1.1k
views
Job:
Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting
CuratedAtlasQueryR
MoleculeExperiment
SingleCellExperiment
SpatialExperiment
19 months ago
Stefano Mangiola
▴ 40
0
votes
0
replies
620
views
Filtering the genesets for fgseaMultiLevel
msigdb
fgsea
msig
19 months ago
Tanvi
• 0
0
votes
1
reply
784
views
Significant genes in DESeq2 analysis
DESeq2
RNASeq
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
cbio
• 0
1
vote
3
replies
2.0k
views
Combining two bulk RNA seq datasets
RNASeqData
DESeq2
Normalization
19 months ago
Tanvi
• 0
2
votes
6
replies
1.6k
views
Create multiple DoparParams with different number of registered cores
BiocParallel
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
ATpoint
★ 5.0k
1
vote
1
reply
878
views
Otsu threshold segmentation using EBImage
EBImage
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
medha.bulusu
• 0
46,732 results • Page
21 of 935
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Answer: lfc shrinkage estimator in DESeq2
by
plumsgorillas
• 0
You are on the right track. In DESeq2, raw log2 fold changes are often noisy and can be misleading, especially for genes with low counts. A…
Answer: Array weights in dpcDE
by
Gordon Smyth
53k
The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. However,…
Answer: lfc shrinkage estimator in DESeq2
by
Michael Love
43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice
by
Gordon Smyth
53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice
by
SamGG
▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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