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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
2
replies
225
views
Regressing out batch effects
DESeq2
updated 17 days ago by
Michael Love
41k • written 23 days ago by
kys91240
• 0
0
votes
2
replies
769
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
168
views
Minfi - estimatecellscount
min
minfi
29 days ago
clacarion
• 0
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 27 days ago by
isaac.vock
• 0 • written 7.9 years ago by
Jon Manning
▴ 90
0
votes
2
replies
175
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
24 days ago
Gimena
• 0
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
2
replies
166
views
Gene Ontology doubt
microbiomeExplorer
26 days ago • updated 22 days ago
Bhawna
• 0
0
votes
2
replies
334
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
5 weeks ago • updated 24 days ago
Gordon
• 0
2
votes
2
replies
151
views
[DiffBind] Obtaining normalization factors
DiffBind
15 days ago • updated 11 days ago
Henry
▴ 10
1
vote
2
replies
97
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
3 days ago • updated 2 days ago
ATpoint
★ 4.0k
1
vote
2
replies
936
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 4 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
2
replies
155
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
4 days ago • updated 2 days ago
shuwangxinze1996
• 0
0
votes
2
replies
238
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
27 days ago • updated 8 days ago
isaac.vock
• 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
1.1k
views
library size and fold changes
edgeR
edgeR
updated 28 days ago by
Gordon Smyth
50k • written 12.4 years ago by
Bogdan
▴ 670
1
vote
2
replies
191
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
9 days ago • updated 8 days ago
Le
• 0
2
votes
2
replies
175
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
15 days ago • updated 14 days ago
julia_mcdonough
• 0
0
votes
2
replies
96
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
8 days ago
prity6459
• 0
1
vote
2
replies
129
views
Error in champ.load(): The following specified files do not exist
ChAMP
9 days ago
Sherin
• 0
0
votes
2
replies
692
views
biomart not ound some prevous release
biomart
rnaseq
written 5.2 years ago by
jarod_v6@libero.it
▴ 40
0
votes
1
reply
115
views
Deseq2 Rlog transformation
DESeq2
updated 12 days ago by
ATpoint
★ 4.0k • written 13 days ago by
Sahar
• 0
0
votes
1
reply
124
views
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
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
1
vote
1
reply
155
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
1
vote
1
reply
166
views
Differentially expressed genes in monocle pseudotime
monocle
updated 11 days ago by
Gordon Smyth
50k • written 13 days ago by
kthapa
• 0
1
vote
1
reply
57
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 19 hours ago by
Leo Lahti
▴ 40 • written 1 day ago by
Dario Strbenac
★ 1.5k
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
1
reply
127
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 11 days ago by
kamryncole1963
• 0 • written 16 days ago by
Sara
• 0
0
votes
1
reply
86
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 2 days ago by
Michael Love
41k • written 3 days ago by
kcarey
• 0
0
votes
1
reply
91
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 9 days ago by
Alejandro Reyes
★ 1.9k • written 9 days ago by
Alessia
• 0
3
votes
1
reply
234
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
i.sudbery
▴ 40
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 19 days ago by
BCS12
• 0
0
votes
1
reply
136
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
zh9118
• 0
0
votes
1
reply
121
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 11 days ago by
James W. MacDonald
65k • written 14 days ago by
tian.liu0720
• 0
0
votes
1
reply
103
views
what is the sampleFiles
chipseq
updated 11 days ago by
James W. MacDonald
65k • written 11 days ago by
zhulin
• 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 23 days ago by
Kim
• 0
0
votes
1
reply
139
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 13 days ago by
Guido Hooiveld
★ 3.9k • written 17 days ago by
Lucie
• 0
0
votes
1
reply
83
views
Input Question for deseq.r
RSeqAn
updated 9 days ago by
ATpoint
★ 4.0k • written 10 days ago by
Nina
• 0
0
votes
1
reply
98
views
rlog transformation
DESeq2
updated 9 days ago by
Michael Love
41k • written 9 days ago by
ishij9717
• 0
0
votes
1
reply
124
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 9 days ago by
ATpoint
★ 4.0k • written 10 days ago by
quanah.hudson
• 0
0
votes
1
reply
161
views
DESeq2 gives an error and R crashes
DESeq2
16 days ago • updated 15 days ago
Shefali
• 0
1
vote
1
reply
101
views
Citation for edgeR user guide
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
k___
▴ 30
0
votes
1
reply
117
views
covariate with negative and positive values
DESeq2
updated 9 days ago by
Michael Love
41k • written 10 days ago by
Brynn
• 0
0
votes
1
reply
102
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 4 days ago by
Gordon Smyth
50k • written 4 days ago by
taur.vil
• 0
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 14 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
62
views
ATACseq merge peaks
DiffBind
updated 1 day ago by
ATpoint
★ 4.0k • written 3 days ago by
Shloka
• 0
0
votes
1
reply
100
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 1 day ago by
Gordon Smyth
50k • written 5 days ago by
Lluís Revilla Sancho
▴ 730
3
votes
1
reply
127
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 8 days ago by
Gordon Smyth
50k • written 9 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
119
views
Granges regionCounts not returning the expected number of entries
methylKit
22 days ago • updated 21 days ago
Modoc Kesner
▴ 10
194 results • Page
3 of 4
Recent ...
Replies
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…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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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