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Views
Votes
0
votes
0
replies
88
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
20 days ago
Stevie Pederson
• 0
2
votes
2
replies
378
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
20 days ago • updated 19 days ago
Henry
▴ 10
0
votes
0
replies
96
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
20 days ago
communication
• 0
4
votes
8
replies
382
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 13 days ago by
Peter Hickey
▴ 740 • written 20 days ago by
Juan Higareda
• 0
3
votes
6
replies
264
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
20 days ago
nhaus
▴ 30
0
votes
1
reply
136
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 16 days ago by
kamryncole1963
• 0 • written 20 days ago by
Sara
• 0
0
votes
1
reply
172
views
DESeq2 gives an error and R crashes
DESeq2
21 days ago • updated 20 days ago
Shefali
• 0
1
vote
2
replies
237
views
How to retrieve detailed regression results from deseq2
DESeq2
21 days ago • updated 12 days ago
Weiqian
▴ 10
5
votes
9
replies
896
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
21 days ago • updated 13 days ago
Chris
• 0
0
votes
0
replies
126
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
21 days ago
Eryn
• 0
0
votes
0
replies
84
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
21 days ago
Dennis
• 0
0
votes
1
reply
153
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 17 days ago by
Guido Hooiveld
★ 3.9k • written 21 days ago by
Lucie
• 0
0
votes
4
replies
218
views
Storing directories inside an ExperimentHub package?
ExperimentHub
21 days ago • updated 20 days ago
Tim Barry
• 0
8
votes
23
replies
911
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 20 days ago by
Robert Castelo
★ 3.3k • written 21 days ago by
Bine
▴ 40
1
vote
3
replies
340
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 16 days ago by
Gordon Smyth
50k • written 22 days ago by
Simran
• 0
0
votes
1
reply
146
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
zh9118
• 0
0
votes
1
reply
156
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 22 days ago by
Michael Love
41k • written 22 days ago by
Adelaide
• 0
5
votes
6
replies
413
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 19 days ago by
ATpoint
★ 4.1k • written 22 days ago by
nhaus
▴ 30
0
votes
0
replies
105
views
ggtree tip label position (depth)
ggtree
22 days ago
Roope
• 0
1
vote
6
replies
475
views
GSVA on separate healthy and disease datasets
GSVA
updated 21 days ago by
James W. MacDonald
65k • written 22 days ago by
Lucy
▴ 60
2
votes
6
replies
384
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
23 days ago
Chris
• 0
0
votes
1
reply
133
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 21 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Merav
• 0
0
votes
0
replies
139
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
23 days ago
arne.sahm
• 0
0
votes
0
replies
94
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
23 days ago
Wolfgang Huber
★ 13k
3
votes
3
replies
313
views
permutation test in edgeR
rna-seq
edgeR
updated 11 days ago by
Gordon Smyth
50k • written 24 days ago by
Netanel
• 0
0
votes
1
reply
175
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 23 days ago by
James W. MacDonald
65k • written 24 days ago by
BCS12
• 0
0
votes
1
reply
157
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 26 days ago by
Gordon Smyth
50k • written 26 days ago by
avery
• 0
0
votes
4
replies
301
views
Help with design.matrix
limma
26 days ago • updated 25 days ago
andrea.rodriguez-martinez13
• 0
1
vote
3
replies
240
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
Shaimaa Gamal
• 0
0
votes
0
replies
140
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
26 days ago
andromeda
• 0
0
votes
2
replies
156
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
joshua.mannheimer
• 0
0
votes
2
replies
213
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 22 days ago by
Michael Love
41k • written 26 days ago by
nhaus
▴ 30
2
votes
2
replies
183
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 26 days ago by
ATpoint
★ 4.1k • written 27 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
126
views
Granges regionCounts not returning the expected number of entries
methylKit
27 days ago • updated 26 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
98
views
flowDensity on a flowset
flowDensity
27 days ago
fredrikwallberg
• 0
0
votes
2
replies
232
views
Regressing out batch effects
DESeq2
updated 22 days ago by
Michael Love
41k • written 27 days ago by
kys91240
• 0
1
vote
1
reply
160
views
DESeq2 - Missing values in count matrix
DESeq2
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
Hong Thu
• 0
0
votes
0
replies
85
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
28 days ago
Macsue
• 0
0
votes
1
reply
231
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 28 days ago by
Tim Peters
▴ 170 • written 28 days ago by
Kim
• 0
1
vote
6
replies
418
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 28 days ago by
Michael Love
41k • written 28 days ago by
RL
• 0
1
vote
4
replies
426
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 27 days ago by
Gordon Smyth
50k • written 28 days ago by
jari.karppinen
• 0
0
votes
2
replies
155
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
28 days ago
Marianna
▴ 20
0
votes
2
replies
182
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
28 days ago
Gimena
• 0
0
votes
6
replies
322
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 21 days ago by
Tim Peters
▴ 170 • written 29 days ago by
s.malik
• 0
1
vote
10
replies
438
views
Obtaining pheno data from CEL files
GEO
affy
29 days ago • updated 22 days ago
Kurtis
• 0
1
vote
1
reply
148
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
29 days ago
Layal
• 0
0
votes
2
replies
166
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
29 days ago
michelafrancesconi8
• 0
0
votes
1
reply
138
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 29 days ago by
James W. MacDonald
65k • written 29 days ago by
Reeya
• 0
0
votes
4
replies
250
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Aidan
• 0
0
votes
4
replies
409
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
4 weeks ago • updated 29 days ago
Lucy
▴ 60
204 results • Page
3 of 5
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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