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Creation
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0
votes
2
replies
836
views
Miss GO accession compare to Gene Ontology website
biomaRt
5.8 years ago
antoineclem1207
• 0
0
votes
2
replies
4.2k
views
Problem installing and loading the package SingleCellExperiment
software error
updated 5.8 years ago by
Aaron Lun
★ 29k • written 5.8 years ago by
NIK
• 0
3
votes
4
replies
1.7k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures
genomicranges
updated 5.8 years ago by
Hervé Pagès
16k • written 5.9 years ago by
Guandong Shang
▴ 40
0
votes
4
replies
1.3k
views
duplicated interactions using package GenomicInteractions
GenomicInteractions
5.8 years ago
chang.jiaming
• 0
0
votes
2
replies
1.0k
views
estimating variability in absence of replicates for edgeR
edgeR
RNAseq
voom
variability estimator
updated 5.8 years ago by
Gordon Smyth
53k • written 5.8 years ago by
hcnbox
• 0
0
votes
4
replies
1.0k
views
.csv files from miRDeep2 to upload in R studio for DESeq2
deseq2
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
ljbond
• 0
0
votes
8
replies
5.6k
views
WGCNA Soft Thresholding: Why does my y-axis for signed R^2 (R-squared) go above 1 and asymptote at 1.5?
WGCNA
Soft Thresholding
updated 5.8 years ago by
Peter Langfelder
★ 3.0k • written 5.8 years ago by
DWF
• 0
0
votes
0
replies
724
views
fit gene distribution to negative binomial
microarray
5.8 years ago
fabien.tell
• 0
0
votes
2
replies
1.5k
views
Limits of log2fold change (30, -30) with DESeq2 results
deseq2
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
r.robertson
• 0
0
votes
2
replies
1.8k
views
WGCNA analysis on RNAseq and proteoimcs data
cancer
updated 4 months ago by
sum31278
• 0 • written 5.8 years ago by
sagigordon
• 0
0
votes
0
replies
1.2k
views
DSS smoothing RRBS and strand collapse
DSS
BSSeq
5.8 years ago
stephanie.rialle
• 0
0
votes
2
replies
651
views
Count outliers differs per design will running DESeq
deseq2
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
MiKappa
▴ 30
0
votes
8
replies
6.5k
views
Combining 2 datasets from 2 different RNAseq experiments
deseq2
normalization
probe
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
l.s.wijaya
• 0
0
votes
1
reply
915
views
Trying to access the source repository of a bioconductor package (Developer Access)
CNORfeeder
CNORode
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
enio.gjerga
• 0
0
votes
1
reply
1.1k
views
Subsetting the bamfile by readlength and extracting the information about distribution the SNV across these reads length
Rsamtools
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
alexandr.gopanenko
▴ 50
0
votes
4
replies
2.0k
views
Issues with normalizing viral-infected single cell data
scan
scater
single cell
normalization
updated 5.8 years ago by
Aaron Lun
★ 29k • written 5.8 years ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
1.7k
views
How can doubletCell() scores be converted to single/doublet annotation?
scran
doublet
updated 5.8 years ago by
Aaron Lun
★ 29k • written 5.8 years ago by
thkapell
▴ 10
4
votes
7
replies
2.0k
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger
differential expression
TCGA
Gene ID
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
fawazfebin
▴ 60
0
votes
3
replies
1.6k
views
Enhanced volcanoplots from DESeq2
EnhancedVolcano
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
rimss.khurana
• 0
2
votes
1
reply
2.0k
views
How do you know if your DESeq2 data has normal distribution?
R
pca
ellipse
normaldistribution
updated 5.8 years ago by
Kevin Blighe
★ 4.0k • written 5.8 years ago by
ecg1g15
▴ 30
0
votes
4
replies
1.9k
views
segfault "memory not mapped" using align from Rsubread
Rsubread
align
5.8 years ago
Joseph Fass
▴ 70
3
votes
6
replies
2.9k
views
paired and unpaired test at the same time with voom limma
limma
voom
rna-seq
paired test
unpaired test
updated 5.8 years ago by
Gordon Smyth
53k • written 5.8 years ago by
dagsbio
• 0
0
votes
0
replies
1.7k
views
from raw reads ASV table - dada2 - small number of merged pairs
dada2
515F - 806Rd
5.8 years ago
beginner87
• 0
2
votes
2
replies
949
views
Input files available for gwasurvivr vignette?
gwasurvivr
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
dec986
• 0
0
votes
1
reply
1.0k
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
5.8 years ago
i.s.castanho
• 0
0
votes
4
replies
1.8k
views
Fonction of genes/metabolites in a pathway?
gene
metabolite
functionnal annotation
pathways
updated 5.8 years ago by
Kevin Blighe
★ 4.0k • written 5.8 years ago by
emisecherre
• 0
0
votes
3
replies
1.6k
views
Error in getBM() for Phytozome
biomaRt
getBM
Phytozome
Chlamydomonas
updated 5.8 years ago by
Mike Smith
★ 6.6k • written 5.8 years ago by
ytlin610
▴ 10
3
votes
5
replies
1.8k
views
Information on genomic sequences via Seqinfo failing
GenomeInfoDb
updated 5.8 years ago by
Hervé Pagès
16k • written 5.8 years ago by
Benilton Carvalho
★ 4.3k
2
votes
3
replies
787
views
Error in getBM
software error
5.8 years ago
gerassimov
▴ 10
1
vote
1
reply
913
views
edgeR DGEList model matrix and experiment design
edgeR
updated 5.8 years ago by
Yunshun Chen
▴ 900 • written 5.8 years ago by
wangjiawen
• 0
0
votes
2
replies
1.2k
views
New package function redistribution
package
license
C
R
5.8 years ago
adam.eleni1
• 0
1
vote
2
replies
855
views
"Blocking" in design matrix prior to limma DE analysis
limma
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
bhakti.dwivedi
• 0
5
votes
5
replies
2.0k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools
huex10sttranscriptcluster.db
affymetrix
Geoquery
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
svlachavas
▴ 840
0
votes
2
replies
604
views
tximport names must be the same length as the vector
r
updated 3.8 years ago by
abradford
• 0 • written 5.8 years ago by
laurie.r.gray
• 0
1
vote
4
replies
1.1k
views
GenomicScores cannot find phastCons30way.UCSC.hg38 though package is loaded
annotation
updated 5.8 years ago by
Robert Castelo
★ 3.4k • written 5.8 years ago by
Paul Shannon
▴ 470
1
vote
1
reply
23k
views
Why does the DESEQ2 lfcshrink function results not include the stat variable
deseq2
stat
lfcshrink
5.8 years ago
divercory
• 0
1
vote
0
replies
977
views
News:
Importing alevin inferential replicates into R with tximport
tximport
News
5.8 years ago
Michael Love
43k
0
votes
3
replies
811
views
DEseq2 design tutorial with multiple experimental factors
deseq2
annotation
normalization
5.8 years ago
christophe.vanhaver
• 0
1
vote
4
replies
1.7k
views
remove background color from dba.plotVolcano (Diffbind)
diffbind
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
hy
• 0
1
vote
2
replies
2.9k
views
Gene Clustering DESeq2 for results
deseq2
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
Matan G.
▴ 60
0
votes
1
reply
3.8k
views
Installation Path Not Writeable
R
BioConductor
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
srinivasan.sandiego
• 0
1
vote
8
replies
13k
views
BioMart: curl option when using getBM in loop
curl
biomart
getBM
Tutorial
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
Ni-Ar
▴ 10
2
votes
1
reply
1.8k
views
Using DESeq2 for normalization of dataset with no replicates
normalization
deseq2
updated 5.8 years ago by
Michael Love
43k • written 5.9 years ago by
Hadi Hosseini
• 0
0
votes
1
reply
960
views
Software package submission: valid push, but not response/review
package submission
review
updated 5.8 years ago by
Hervé Pagès
16k • written 5.8 years ago by
whou10
• 0
0
votes
1
reply
1.4k
views
Estimate cell proportion from beta values using minfi estimateCellCounts?
minfi
cell proportion
estimateCellCounts
DNA Methylation
5.8 years ago
grayapply2009
• 0
0
votes
1
reply
771
views
can not load org.dm.eg.db library
annotation
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
shefy
• 0
1
vote
4
replies
1.7k
views
Nested paired design with covariates in limma
RNA-seq
Nested paired design
limma
updated 3.0 years ago by
Gordon Smyth
53k • written 5.8 years ago by
ibrahim.akkouh
• 0
0
votes
3
replies
2.7k
views
edgeR: "no non-missing arguments to min; returning Inf" after filterByExpression
filterByExpression
edgeR
RNAseq analysis
edger
updated 5.8 years ago by
Gordon Smyth
53k • written 5.8 years ago by
hcnbox
• 0
0
votes
1
reply
1.9k
views
mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest")
deseq2
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
adR
▴ 40
2
votes
4
replies
6.7k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto
tximport
deseq2
counts
6.8 years ago • updated 5.8 years ago
Mozart
▴ 30
46,730 results • Page
174 of 935
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Comment: chemmineOB install help
by
Jeremy
• 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…
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A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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