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Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression
DESeq2
17 months ago • updated 16 months ago
David W. H.
• 0
0
votes
0
replies
804
views
Job:
Postdoc+PhD position: AI large-language models of single-cell data for cancer immunogenomics
JobPosting
AI
HPC
CuratedAtlasQueryR
17 months ago
Stefano Mangiola
▴ 40
0
votes
0
replies
987
views
Job:
Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting
CuratedAtlasQueryR
MoleculeExperiment
SingleCellExperiment
SpatialExperiment
17 months ago
Stefano Mangiola
▴ 40
0
votes
0
replies
559
views
Filtering the genesets for fgseaMultiLevel
msigdb
fgsea
msig
17 months ago
Tanvi
• 0
0
votes
1
reply
724
views
Significant genes in DESeq2 analysis
DESeq2
RNASeq
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
cbio
• 0
1
vote
3
replies
1.9k
views
Combining two bulk RNA seq datasets
RNASeqData
DESeq2
Normalization
17 months ago
Tanvi
• 0
2
votes
6
replies
1.4k
views
Create multiple DoparParams with different number of registered cores
BiocParallel
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
ATpoint
★ 5.0k
1
vote
1
reply
799
views
Otsu threshold segmentation using EBImage
EBImage
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
medha.bulusu
• 0
0
votes
0
replies
672
views
News:
AnnotationHub and ExperimentHub Access Downtime
AnnotationHub
ExperimentHub
17 months ago
shepherl
4.2k
2
votes
2
replies
1.6k
views
biomaRt has encountered an unknown server error while using getLDS
BioMartGOGeneSets
getLDS
17 months ago
miriam.lloriansopena
• 0
0
votes
2
replies
973
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
17 months ago
Mallory
• 0
0
votes
0
replies
769
views
Job:
PhD-position in bioinformatics / computational biology
Epigenomics
NGS
Aging
Biobase
updated 17 months ago by
Michael Love
43k • written 17 months ago by
arne.sahm
• 0
0
votes
0
replies
774
views
ligand-receptor-interactions for bulk RNAseq in R
decoupleR
17 months ago
silvaesilva.da
• 0
0
votes
1
reply
1.3k
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 17 months ago by
Michael Love
43k • written 18 months ago by
prabath_meemaduma
• 0
2
votes
1
reply
681
views
Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 17 months ago by
Michael Love
43k • written 18 months ago by
hx
▴ 10
0
votes
0
replies
626
views
BiomaRt attribute "description" doesn't return NCBI's gene summary anymore
biomaRt
17 months ago
Reese
• 0
2
votes
1
reply
821
views
DESeq2 returns results for group with just one replicate
DESeq2
DifferentialExpression
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
nhaus
▴ 70
3
votes
13
replies
2.0k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq
limma
updated 18 months ago by
Masongeorge
• 0 • written 18 months ago by
ij283
• 0
0
votes
0
replies
469
views
Scoreplot for OPLS
splots
18 months ago
devarti.mahakalkar
• 0
1
vote
2
replies
1.2k
views
GESA with certain gene list returns no result with human genom, but many result with mouse genom.
clusterProfiler
18 months ago • updated 17 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
18 months ago
vohara4
• 0
4
votes
2
replies
1.9k
views
Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor
featurecounts
subread
18 months ago
Rachael
• 0
1
vote
9
replies
3.3k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 17 months ago by
James W. MacDonald
68k • written 18 months ago by
adrip
▴ 10
0
votes
1
reply
874
views
How can I get gseGO to return all GO terms tested?
clusterProfiler
clusterp
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
yesitsjess
• 0
0
votes
0
replies
511
views
Error in drawHeatmap function
GeneOverlap
heatmaps
18 months ago • updated 17 months ago
Johanna
• 0
2
votes
4
replies
1.6k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
20 months ago • updated 17 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 18 months ago by
James W. MacDonald
68k • written 18 months ago by
Ben
▴ 50
1
vote
4
replies
1.5k
views
error loading collectTRI regulon
decoupleR
OmnipathR
18 months ago
silvaesilva.da
• 0
0
votes
4
replies
2.4k
views
Combining analysis of EPICv1 and EPICv2 using SeSAMe package
sesameData
EPICv2
EPICv1
updated 6 months ago by
Mancy
• 0 • written 18 months ago by
archibold.mposhi
• 0
3
votes
6
replies
3.5k
views
Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 18 months ago by
ATpoint
★ 5.0k • written 2.7 years ago by
liuyang32201220
▴ 20
0
votes
7
replies
2.0k
views
EnhancedVolcano results in an empty plot
EnhancedVolcano
18 months ago
Patadù
▴ 20
0
votes
1
reply
773
views
News:
Stop mirror service
metaMSdata
updated 18 months ago by
shepherl
4.2k • written 18 months ago by
khonda
• 0
1
vote
3
replies
1.2k
views
chemmineOB install help
ChemmineOB
Install
18 months ago
jrbald04
• 0
2
votes
2
replies
937
views
Double normalising when using sva and deseq2
DESeq2
Normalisation
Bulkrnaseq
Svaseq
18 months ago
BioinfGuru
▴ 70
2
votes
3
replies
1.0k
views
Can I adjust weights by group in dreamlet(), like in voomByGroup(), with a random effect?
dreamlet
updated 18 months ago by
gabriel.hoffman
▴ 170 • written 18 months ago by
jcollier
• 0
0
votes
1
reply
890
views
Recount3 error downloading data
recount3
recount
updated 18 months ago by
Leonardo Collado Torres
★ 1.1k • written 22 months ago by
Max Bone
• 0
0
votes
1
reply
808
views
When I tried to use the functions from the celldex package to fetch information, I encountered the following error. How can I resolve this?"
celldex
SingleR
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
1319244258
• 0
0
votes
0
replies
474
views
Amplican doesn't recognize forward reads fast q file
amplican
18 months ago
landenshanie
▴ 40
1
vote
2
replies
1.3k
views
Cohen's D calculation for differentially expressed genes via DESeq2 results summary stats
DESeq2
18 months ago
a_p
• 0
1
vote
5
replies
3.2k
views
Issues with installing Bioconductor packages (eg GEOquery)
GEOquery
Bioconductor
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
Isabel
• 0
4
votes
14
replies
2.7k
views
Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() from AnnotationForge
OrganismDb
AnnotationForge
18 months ago
Ozan
• 0
1
vote
2
replies
957
views
Interpretation of GSVA with absRanking=TRUE
GSVA
18 months ago
gad.abraham
• 0
0
votes
1
reply
729
views
Can we compare 3 different experimental conditions with DESeq2?
DESeq2
StatisticalMethod
updated 18 months ago by
swbarnes2
★ 1.4k • written 18 months ago by
Esteban
• 0
0
votes
1
reply
644
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData
DESeq2
DifferentialExpression
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
ZhuYi
• 0
1
vote
2
replies
2.8k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 18 months ago by
rodrigo.duarte88
▴ 40 • written 6.1 years ago by
mohamedrefaat.1.1992
• 0
0
votes
1
reply
534
views
How to access the Bioconductor in Windows
Bioconductor
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
fahad.rashid
• 0
0
votes
3
replies
883
views
STRINGdb server response time for mapping
mapping
serverresponsetime
STRINGdb
updated 18 months ago by
damian.szk
▴ 110 • written 18 months ago by
roberto.pellegrino
• 0
3
votes
6
replies
1.4k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
18 months ago
JG13
• 0
0
votes
0
replies
829
views
Job:
Group Leader (Faculty) positions at EMBL-EBI, Cambridge UK
research
exciting
career
escape
18 months ago
Wolfgang Huber
★ 13k
1
vote
3
replies
927
views
STRINGdb v.2.16.4 does not render the plot [libpng error: Not a PNG file]
STRINGdb
updated 18 months ago by
damian.szk
▴ 110 • written 18 months ago by
h.valipour.k
• 0
46,691 results • Page
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Answer: PTM analysis in LIMPA
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53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
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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
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