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0
votes
1
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124
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Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 17 days ago by
ATpoint
★ 4.0k • written 19 days ago by
Merav
• 0
0
votes
0
replies
127
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
19 days ago
arne.sahm
• 0
0
votes
0
replies
85
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
19 days ago
Wolfgang Huber
★ 13k
3
votes
3
replies
295
views
permutation test in edgeR
rna-seq
edgeR
updated 6 days ago by
Gordon Smyth
50k • written 19 days ago by
Netanel
• 0
0
votes
1
reply
167
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 19 days ago by
James W. MacDonald
65k • written 20 days ago by
BCS12
• 0
0
votes
1
reply
150
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 21 days ago by
Gordon Smyth
50k • written 22 days ago by
avery
• 0
0
votes
4
replies
291
views
Help with design.matrix
limma
22 days ago • updated 21 days ago
andrea.rodriguez-martinez13
• 0
1
vote
3
replies
231
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
Shaimaa Gamal
• 0
0
votes
0
replies
134
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
22 days ago
andromeda
• 0
0
votes
2
replies
148
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
joshua.mannheimer
• 0
0
votes
2
replies
202
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 17 days ago by
Michael Love
41k • written 22 days ago by
nhaus
▴ 30
2
votes
2
replies
171
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 22 days ago by
ATpoint
★ 4.0k • written 22 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
119
views
Granges regionCounts not returning the expected number of entries
methylKit
23 days ago • updated 22 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
88
views
flowDensity on a flowset
flowDensity
23 days ago
fredrikwallberg
• 0
0
votes
2
replies
225
views
Regressing out batch effects
DESeq2
updated 18 days ago by
Michael Love
41k • written 23 days ago by
kys91240
• 0
1
vote
1
reply
156
views
DESeq2 - Missing values in count matrix
DESeq2
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
Hong Thu
• 0
0
votes
0
replies
80
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
23 days ago
Macsue
• 0
0
votes
1
reply
218
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 23 days ago by
Tim Peters
▴ 170 • written 24 days ago by
Kim
• 0
1
vote
6
replies
407
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 23 days ago by
Michael Love
41k • written 24 days ago by
RL
• 0
1
vote
4
replies
417
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 23 days ago by
Gordon Smyth
50k • written 24 days ago by
jari.karppinen
• 0
0
votes
2
replies
148
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
24 days ago
Marianna
▴ 20
0
votes
2
replies
176
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
24 days ago
Gimena
• 0
0
votes
6
replies
315
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 17 days ago by
Tim Peters
▴ 170 • written 25 days ago by
s.malik
• 0
1
vote
10
replies
411
views
Obtaining pheno data from CEL files
GEO
affy
25 days ago • updated 18 days ago
Kurtis
• 0
1
vote
1
reply
139
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
25 days ago • updated 24 days ago
Layal
• 0
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
25 days ago • updated 24 days ago
michelafrancesconi8
• 0
0
votes
1
reply
129
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 25 days ago by
James W. MacDonald
65k • written 25 days ago by
Reeya
• 0
0
votes
4
replies
235
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 25 days ago by
Michael Love
41k • written 26 days ago by
Aidan
• 0
0
votes
1
reply
99
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
Leyre
• 0
0
votes
4
replies
396
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
26 days ago • updated 25 days ago
Lucy
▴ 60
0
votes
2
replies
168
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
26 days ago • updated 25 days ago
Seongsu
• 0
0
votes
1
reply
145
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 25 days ago by
James W. MacDonald
65k • written 27 days ago by
ja569116
• 0
0
votes
2
replies
166
views
Gene Ontology doubt
microbiomeExplorer
27 days ago • updated 23 days ago
Bhawna
• 0
0
votes
2
replies
277
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
27 days ago • updated 22 days ago
fer_talavera
• 0
1
vote
2
replies
206
views
MethylKit read issue
methylKit
updated 22 days ago by
James W. MacDonald
65k • written 27 days ago by
CHEN
• 0
0
votes
2
replies
239
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
27 days ago • updated 8 days ago
isaac.vock
• 0
0
votes
7
replies
354
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
28 days ago • updated 25 days ago
needNGS
• 0
0
votes
1
reply
159
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 26 days ago by
Michael Love
41k • written 29 days ago by
saadmurtazakhan
▴ 10
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
29 days ago • updated 7 days ago
Chris
• 0
0
votes
2
replies
168
views
Minfi - estimatecellscount
min
minfi
29 days ago
clacarion
• 0
0
votes
0
replies
100
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
29 days ago
feather-W
• 0
0
votes
0
replies
100
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
29 days ago
Ankit
▴ 20
1
vote
5
replies
308
views
fgsea fork
fgsea
updated 29 days ago by
James W. MacDonald
65k • written 29 days ago by
yimjohns
• 0
3
votes
5
replies
352
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 28 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Fabian
• 0
0
votes
6
replies
327
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 29 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Faisal
• 0
0
votes
1
reply
147
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Mikushi
• 0
0
votes
2
replies
220
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
4 weeks ago • updated 25 days ago
w.cookson
• 0
0
votes
0
replies
87
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
4 weeks ago
Pierre Lindenbaum
▴ 10
0
votes
1
reply
125
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Karen
• 0
2
votes
3
replies
336
views
PCA of different bacterial species
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Laura
▴ 10
45,581 results • Page
3 of 912
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Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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