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0
votes
2
replies
265
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
25 days ago • updated 23 days ago
shuwangxinze1996
• 0
0
votes
2
replies
122
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 3 days ago by
zhouwanding
▴ 10 • written 5 days ago by
Seungmin
• 0
1
vote
2
replies
212
views
Improving the design matrices vignette in RNAseq123
RNAseq123
26 days ago • updated 11 days ago
Lluís Revilla Sancho
▴ 730
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 7 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
2
replies
132
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 4 hours ago by
JKim
• 0 • written 23 hours ago by
Ken C
• 0
1
vote
2
replies
226
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
4 days ago • updated 1 day ago
BioinfGuru
▴ 30
0
votes
2
replies
99
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
1 day ago
makala
• 0
0
votes
2
replies
818
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
0
votes
2
replies
929
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.3 years ago by
araaaju
• 0
0
votes
2
replies
237
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
28 days ago • updated 25 days ago
catv
• 0
0
votes
2
replies
947
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 2 days ago by
mariakenneth147
• 0 • written 17 months ago by
pharamac
• 0
1
vote
2
replies
738
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 21 days ago
Patadù
▴ 10
1
vote
2
replies
398
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
Kim
• 0
0
votes
2
replies
190
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 25 days ago by
taur.vil
• 0
1
vote
2
replies
369
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 14 days ago
Kim
• 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 17 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 0
2
votes
2
replies
224
views
fgsea significant result
fgsea
13 days ago • updated 12 days ago
Chris
▴ 10
0
votes
2
replies
91
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
4 days ago • updated 3 days ago
Yveto
• 0
2
votes
2
replies
271
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
10 days ago • updated 5 days ago
zzrammal
• 0
0
votes
2
replies
281
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
6 weeks ago • updated 28 days ago
isaac.vock
• 0
2
votes
2
replies
234
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
18 days ago
Chris
▴ 10
0
votes
2
replies
226
views
PCA plot suggestions
DESeq2
PCAtools
updated 21 days ago by
Michael Love
42k • written 23 days ago by
Aaliya
• 0
0
votes
2
replies
147
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
29 days ago
prity6459
• 0
0
votes
2
replies
160
views
DESeq2 v1.35.0
DESeq2
updated 15 days ago by
Michael Love
42k • written 15 days ago by
Espresso
• 0
0
votes
2
replies
749
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 2 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
257
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
9 days ago • updated 8 days ago
Dylan.Sheerin
• 0
2
votes
1
reply
67
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 2 days ago by
Alejandro Reyes
★ 1.9k • written 4 days ago by
Sara
• 0
1
vote
1
reply
152
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 21 days ago by
Leo Lahti
▴ 40 • written 21 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
154
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
c53aba27
• 0
0
votes
1
reply
161
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 8 days ago by
ATpoint
★ 4.1k • written 8 days ago by
sajadahmad41454
• 0
2
votes
1
reply
141
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 11 days ago by
Michael Love
42k • written 11 days ago by
mat149
▴ 70
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
z_bahari
• 0
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 10 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 24 days ago by
Michael Love
42k • written 24 days ago by
i.sudbery
▴ 40
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 23 days ago by
Michael Love
42k • written 23 days ago by
kcarey
• 0
0
votes
1
reply
262
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
SSSJec
• 0
0
votes
1
reply
136
views
FDR via q-value
qvalue
updated 25 days ago by
James W. MacDonald
65k • written 28 days ago by
John
• 0
3
votes
1
reply
147
views
How to save the DEXSeq results
DEXSeq
updated 11 days ago by
Michael Love
42k • written 11 days ago by
Sara
• 0
1
vote
1
reply
155
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 17 days ago by
Michael Love
42k • written 17 days ago by
marcusn
• 0
0
votes
1
reply
124
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 29 days ago by
Michael Love
42k • written 29 days ago by
09191919
• 0
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
0
votes
1
reply
123
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 5 days ago by
Guido Hooiveld
★ 4.0k • written 5 days ago by
aogunbaw
• 0
0
votes
1
reply
170
views
ATACseq merge peaks
DiffBind
updated 21 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Shloka
• 0
0
votes
1
reply
135
views
putting my own expression data in deseq2
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Dev
• 0
0
votes
1
reply
131
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 15 days ago by
4r-rtg
• 0
0
votes
1
reply
84
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 3 days ago by
Michael Love
42k • written 4 days ago by
piemmea
• 0
2
votes
1
reply
165
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 10 days ago by
James W. MacDonald
65k • written 11 days ago by
e1271094
• 0
0
votes
1
reply
52
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
16 hours ago • updated 15 hours ago
shaunpeterson
• 0
1
vote
1
reply
185
views
Handling multiple differential expression comparisons
DESeq2
updated 12 days ago by
Michael Love
42k • written 14 days ago by
Zainab
▴ 10
190 results • Page
3 of 4
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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