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0
votes
0
replies
846
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
18 months ago
gamma.jian
▴ 10
1
vote
2
replies
3.4k
views
Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
18 months ago
sropri
• 0
0
votes
5
replies
1.1k
views
modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 18 months ago by
Peter Hickey
▴ 760 • written 18 months ago by
Lluís Revilla Sancho
▴ 760
1
vote
4
replies
2.5k
views
SeSAMe DMR for EPIC V2
sesame
EPICv2manifest
epicv2
updated 5 months ago by
MargaretJDinan
• 0 • written 18 months ago by
luca.s
▴ 50
1
vote
5
replies
2.2k
views
EnsDb: bad_weak_ptr
AnnotationHub
BiocFileCache
18 months ago
Lluís Revilla Sancho
▴ 760
0
votes
5
replies
2.2k
views
Cannot connect to annotationhub server
AnnotationHub
ExperimentHub
updated 18 months ago by
shepherl
4.2k • 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
18 months ago
sukeshinik5
▴ 20
0
votes
0
replies
491
views
Structural Variant Format Converted for BRASS Format
StructuralVariantAnnotation
18 months ago
Dario Strbenac
★ 1.6k
0
votes
1
reply
604
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 18 months ago by
James W. MacDonald
68k • written 18 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
18 months ago
Svitlana
▴ 10
0
votes
0
replies
498
views
Differential Gene Wrapper for Propotion of Detected
scran
18 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 • updated 18 months ago
egbastakis
• 0
4
votes
4
replies
1.2k
views
Warning message when running limma with covariates
limma
18 months ago • updated 12 months ago
Chris
▴ 20
0
votes
9
replies
1.5k
views
Research Project - Expanding search funtionality on the GEO database
GEOquery
GEO
18 months ago
gallantk5
• 0
3
votes
5
replies
3.6k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 18 months ago by
Reza Ghamsari
• 0 • written 22 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
18 months ago
jiachengd
• 0
5
votes
5
replies
1.8k
views
Limma with covariates
limma
written 18 months ago by
Chris
▴ 20
1
vote
1
reply
813
views
DESeq2 - vst() - log2FC - no replicates
DESeq2
log2FC
vst()
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
lifeonmars
• 0
0
votes
2
replies
1.3k
views
Epicv2 conversion fail
minfi
18 months ago
Alex
• 0
1
vote
5
replies
1.2k
views
DESeq2 ML Query
DESeq2
updated 18 months ago by
Michael Love
43k • written 18 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
849
views
Job:
Postdoc+PhD position: AI large-language models of single-cell data for cancer immunogenomics
JobPosting
AI
HPC
CuratedAtlasQueryR
19 months ago • updated 18 months ago
Stefano Mangiola
▴ 40
0
votes
0
replies
1.0k
views
Job:
Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting
CuratedAtlasQueryR
MoleculeExperiment
SingleCellExperiment
SpatialExperiment
19 months ago • updated 18 months ago
Stefano Mangiola
▴ 40
0
votes
0
replies
599
views
Filtering the genesets for fgseaMultiLevel
msigdb
fgsea
msig
19 months ago
Tanvi
• 0
0
votes
1
reply
768
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
841
views
Otsu threshold segmentation using EBImage
EBImage
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
medha.bulusu
• 0
0
votes
0
replies
695
views
News:
AnnotationHub and ExperimentHub Access Downtime
AnnotationHub
ExperimentHub
19 months ago
shepherl
4.2k
2
votes
2
replies
1.7k
views
biomaRt has encountered an unknown server error while using getLDS
BioMartGOGeneSets
getLDS
19 months ago
miriam.lloriansopena
• 0
0
votes
2
replies
1.0k
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
19 months ago
Mallory
• 0
0
votes
0
replies
797
views
Job:
PhD-position in bioinformatics / computational biology
Epigenomics
NGS
Aging
Biobase
updated 19 months ago by
Michael Love
43k • written 19 months ago by
arne.sahm
• 0
0
votes
0
replies
819
views
ligand-receptor-interactions for bulk RNAseq in R
decoupleR
19 months ago
silvaesilva.da
• 0
0
votes
1
reply
1.4k
views
In a 3 group DEG analysis with three batches, can I use 1 group in all three batches to correct for the batch effect?
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
prabath_meemaduma
• 0
2
votes
1
reply
700
views
Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
hx
▴ 10
0
votes
0
replies
657
views
BiomaRt attribute "description" doesn't return NCBI's gene summary anymore
biomaRt
19 months ago
Reese
• 0
2
votes
1
reply
869
views
DESeq2 returns results for group with just one replicate
DESeq2
DifferentialExpression
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
nhaus
▴ 70
3
votes
13
replies
2.1k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq
limma
updated 19 months ago by
Masongeorge
• 0 • written 19 months ago by
ij283
• 0
0
votes
0
replies
501
views
Scoreplot for OPLS
splots
19 months ago
devarti.mahakalkar
• 0
1
vote
2
replies
1.3k
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
19 months ago
sawa
• 0
0
votes
4
replies
1.3k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression
scran
scater
SingleCellExperiment
edgeR
19 months ago
vohara4
• 0
4
votes
2
replies
2.2k
views
Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor
featurecounts
subread
19 months ago
Rachael
• 0
1
vote
9
replies
3.6k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
adrip
▴ 10
0
votes
1
reply
936
views
How can I get gseGO to return all GO terms tested?
clusterProfiler
clusterp
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
yesitsjess
• 0
0
votes
0
replies
528
views
Error in drawHeatmap function
GeneOverlap
heatmaps
19 months ago
Johanna
• 0
2
votes
4
replies
1.7k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
21 months ago • updated 19 months ago
isaac.vock
• 0
1
vote
3
replies
1.1k
views
Including infectivity information to RNA-Seq analysis
RNASeqData
DESeq2
RNA-Seq
RNASeq
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Ben
▴ 50
1
vote
4
replies
1.7k
views
error loading collectTRI regulon
decoupleR
OmnipathR
19 months ago
silvaesilva.da
• 0
0
votes
4
replies
2.5k
views
Combining analysis of EPICv1 and EPICv2 using SeSAMe package
sesameData
EPICv2
EPICv1
updated 7 months ago by
Mancy
• 0 • written 19 months ago by
archibold.mposhi
• 0
3
votes
6
replies
3.7k
views
Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 19 months ago by
ATpoint
★ 5.0k • written 2.8 years ago by
liuyang32201220
▴ 20
46,711 results • Page
21 of 935
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Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures
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ferran.llobet.cabau
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Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
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★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
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jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
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A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
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