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 ★ 29k • written 5.8 years ago by • 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 16k • written 5.9 years ago by ▴ 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 53k • written 5.8 years ago by • 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 43k • written 5.8 years ago by • 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 ★ 3.0k • written 5.8 years ago by • 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 43k • written 5.8 years ago by • 0
0
votes
2
replies
1.8k
views
WGCNA analysis on RNAseq and proteoimcs data
cancer
updated 4 months ago by • 0 • written 5.8 years ago by • 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 43k • written 5.8 years ago by ▴ 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 43k • written 5.8 years ago by • 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 68k • written 5.8 years ago by • 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 25k • written 5.8 years ago by ▴ 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 ★ 29k • written 5.8 years ago by ★ 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 ★ 29k • written 5.8 years ago by ▴ 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 68k • written 5.8 years ago by ▴ 60
0
votes
3
replies
1.6k
views
Enhanced volcanoplots from DESeq2
EnhancedVolcano
updated 5.8 years ago by 43k • written 5.8 years ago by • 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 ★ 4.0k • written 5.8 years ago by ▴ 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 53k • written 5.8 years ago by • 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 68k • written 5.8 years ago by • 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 ★ 4.0k • written 5.8 years ago by • 0
0
votes
3
replies
1.6k
views
Error in getBM() for Phytozome
biomaRt getBM Phytozome Chlamydomonas
updated 5.8 years ago by ★ 6.6k • written 5.8 years ago by ▴ 10
3
votes
5
replies
1.8k
views
Information on genomic sequences via Seqinfo failing
GenomeInfoDb
updated 5.8 years ago by 16k • written 5.8 years ago by ★ 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 ▴ 900 • written 5.8 years ago by • 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 68k • written 5.8 years ago by • 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 68k • written 5.8 years ago by ▴ 840
0
votes
2
replies
604
views
tximport names must be the same length as the vector
r
updated 3.8 years ago by • 0 • written 5.8 years ago by • 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 ★ 3.4k • written 5.8 years ago by ▴ 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 68k • written 5.8 years ago by • 0
1
vote
2
replies
2.9k
views
Gene Clustering DESeq2 for results
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 60
0
votes
1
reply
3.8k
views
Installation Path Not Writeable
R BioConductor
updated 5.8 years ago by 68k • written 5.8 years ago by • 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 68k • written 5.8 years ago by ▴ 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 43k • written 5.9 years ago by • 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 16k • written 5.8 years ago by • 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 25k • written 5.8 years ago by • 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 53k • written 5.8 years ago by • 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 53k • written 5.8 years ago by • 0
0
votes
1
reply
1.9k
views
mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest")
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 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
Recent ...
Replies
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…
Votes
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
Awards • All
Popular Question to ATpoint ★ 5.0k
Popular Question to Martin Morgan 25k
Teacher to Michael Love 43k
Popular Question to A • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Locations • All
Switzerland, 12 minutes ago
The city by the bay, 21 minutes ago
Vietnam, 2 hours ago
Singapore, 2 hours ago
United States, 3 hours ago
Traffic: 735 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6