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1
vote
2
replies
219
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
18 days ago • updated 17 days ago
Le
• 0
1
vote
2
replies
229
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
5 days ago • updated 4 days ago
Yveto
• 0
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
25 days ago • updated 17 days ago
Weiqian
▴ 10
0
votes
2
replies
122
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
6 days ago • updated 3 days ago
Aurora
• 0
0
votes
2
replies
249
views
Regressing out batch effects
DESeq2
updated 26 days ago by
Michael Love
41k • written 4 weeks ago by
kys91240
• 0
0
votes
2
replies
103
views
DESeq2 v1.35.0
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
Espresso
• 0
2
votes
2
replies
390
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
25 days ago • updated 24 days ago
Henry
▴ 10
2
votes
2
replies
195
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
7 days ago • updated 6 days ago
Chris
• 0
1
vote
2
replies
331
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
Kim
• 0
2
votes
2
replies
118
views
fgsea significant result
fgsea
1 day ago
Chris
• 0
2
votes
2
replies
172
views
[DiffBind] Obtaining normalization factors
DiffBind
24 days ago • updated 20 days ago
Henry
▴ 10
1
vote
2
replies
301
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
4 weeks ago • updated 2 days ago
Kim
• 0
1
vote
2
replies
140
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
20 days ago
Ana
• 0
0
votes
2
replies
248
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
13 days ago • updated 11 days ago
shuwangxinze1996
• 0
0
votes
2
replies
256
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
5 weeks ago • updated 17 days ago
isaac.vock
• 0
1
vote
2
replies
197
views
Design Matrix within group comparison more than two groups
DESeq2
24 days ago • updated 23 days ago
hemantcnaik
• 0
2
votes
2
replies
191
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
sansan
• 0
3
votes
2
replies
217
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 14 days ago by
Guido Hooiveld
★ 3.9k • written 16 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
213
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
17 days ago • updated 14 days ago
catv
• 0
0
votes
1
reply
134
views
covariate with negative and positive values
DESeq2
updated 18 days ago by
Michael Love
41k • written 19 days ago by
Brynn
• 0
0
votes
1
reply
145
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 20 days ago by
kamryncole1963
• 0 • written 25 days ago by
Sara
• 0
0
votes
1
reply
121
views
what is the sampleFiles
chipseq
updated 20 days ago by
James W. MacDonald
65k • written 20 days ago by
zhulin
• 0
0
votes
1
reply
103
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
Agung
• 0
1
vote
1
reply
108
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
marcusn
• 0
0
votes
1
reply
107
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
z_bahari
• 0
0
votes
1
reply
708
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 23 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
1
reply
112
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
88
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 6 days ago by
shepherl
3.9k • written 6 days ago by
bounlu
• 0
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 23 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
133
views
Bioinformatics student
Des
DESeq2
updated 24 days ago by
hemantcnaik
• 0 • written 24 days ago by
Sahar
• 0
1
vote
1
reply
179
views
Citation for edgeR user guide
edgeR
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
k___
▴ 30
0
votes
1
reply
149
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 18 days ago by
ATpoint
★ 4.1k • written 19 days ago by
quanah.hudson
• 0
0
votes
1
reply
156
views
Adding columns to DEXSeqResults object
DEXSeq
updated 18 days ago by
Alejandro Reyes
★ 1.9k • written 20 days ago by
Clyde
• 0
0
votes
1
reply
511
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 27 days ago by
ivorychan7777
• 0 • written 15 months ago by
609b0d25
• 0
0
votes
1
reply
160
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 22 days ago by
Guido Hooiveld
★ 3.9k • written 26 days ago by
Lucie
• 0
0
votes
1
reply
139
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 20 days ago by
James W. MacDonald
65k • written 23 days ago by
tian.liu0720
• 0
0
votes
1
reply
101
views
Input Question for deseq.r
RSeqAn
updated 18 days ago by
ATpoint
★ 4.1k • written 19 days ago by
Nina
• 0
0
votes
1
reply
19
views
Help with running egsea()
EGSEA
updated just now by
James W. MacDonald
65k • written 1 hour ago by
Chris
• 0
0
votes
1
reply
137
views
rlog transformation
DESeq2
updated 18 days ago by
Michael Love
41k • written 18 days ago by
ishij9717
• 0
0
votes
1
reply
64
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 4 days ago by
4r-rtg
• 0
0
votes
1
reply
132
views
Deseq2 Rlog transformation
DESeq2
updated 21 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Sahar
• 0
0
votes
1
reply
127
views
FDR via q-value
qvalue
updated 14 days ago by
James W. MacDonald
65k • written 17 days ago by
John
• 0
0
votes
1
reply
101
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
c53aba27
• 0
0
votes
1
reply
177
views
DESeq2 gives an error and R crashes
DESeq2
25 days ago • updated 24 days ago
Shefali
• 0
0
votes
1
reply
138
views
ATACseq merge peaks
DiffBind
updated 10 days ago by
ATpoint
★ 4.1k • written 12 days ago by
Shloka
• 0
0
votes
1
reply
109
views
putting my own expression data in deseq2
DESeq2
updated 6 days ago by
ATpoint
★ 4.1k • written 6 days ago by
Dev
• 0
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 11 days ago by
Michael Love
41k • written 12 days ago by
kcarey
• 0
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
48
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 5 hours ago by
Michael Love
41k • written 6 hours ago by
mat149
▴ 70
0
votes
1
reply
228
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
SSSJec
• 0
195 results • Page
3 of 4
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I am working with mouse data. I don't know how to do this, but I will go through it. Can you help me with the second question? how do we …
Comment: [Mfuzz] Error in cmeans(exprs(eset)
by
Caio
• 0
You can have this problem (lines with variance equal to zero) when you run experiments and obtain the data with more samples and use fewer …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
The left plot indicates you should use genome segmentation. It is what is called "nonstationary" meaning it looks like there are distinct r…
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
gene_bioconductor
▴ 10
Thanks for your thoughtful and detailed comment, Gordon
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Votes
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
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