0
votes
1
reply
1.8k
views
XCMS - cannot allocate vector of size **Gb when global environment is empty
r xcms
6.5 years ago garfield320 ▴ 30
8
votes
8
replies
9.8k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 6.5 years ago by ▴ 40 • written 10.3 years ago by ▴ 50
2
votes
4
replies
4.6k
views
How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 24 months ago by 53k • written 6.5 years ago by • 0
1
vote
7
replies
2.9k
views
How to merge two tximport object into one dataset for DESeqDataSetFromTximport
deseq2 tximport
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
8
votes
8
replies
13k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2 DESeq2
updated 2.4 years ago by • 0 • written 6.5 years ago by ▴ 40
3
votes
3
replies
1.4k
views
DESeq2: Sample outlier patterns 'switching' after normalization
deseq2 normalization
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 40
1
vote
4
replies
1.2k
views
Interpretation of the heatmap produced by DESeq2
DESeq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
0
replies
932
views
Job: Postdoc position at Icahn School of Medicine at Mount Sinai
postdocs Job
6.5 years ago mayte.suarezfarinas • 0
1
vote
2
replies
1.5k
views
Testing random effects in limma
limma
6.5 years ago c.taylor • 0
3
votes
1
reply
1.8k
views
error pushing to git/bioconductor
git AnalysisPageServer
updated 6.5 years ago by ★ 6.6k • written 6.5 years ago by ▴ 10
6
votes
10
replies
6.7k
views
goana and "No annotated genes found in universe" even with Entrez gene ids
goana edger
updated 4.0 years ago by 53k • written 6.5 years ago by ▴ 10
0
votes
2
replies
1.9k
views
cpg.annotate model requirements
DMRcate ChAMP
updated 6.5 years ago by ▴ 290 • written 6.5 years ago by • 0
0
votes
1
reply
3.0k
views
cnetplot graph independently.
go annotation
updated 6.5 years ago by • 0 • written 6.5 years ago by • 0
1
vote
2
replies
708
views
too few replicates to observe statistically significant differences
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
3
replies
1.2k
views
deseq2 formula design
deseq2
updated 6.5 years ago by ★ 1.4k • written 6.5 years ago by ▴ 10
0
votes
1
reply
638
views
Mr. Anjan Payra
software error
6.5 years ago anjan.payra • 0
1
vote
7
replies
2.0k
views
Cannot generate a DEseq2DataSet from my data - DESeqDataSetFromMatrix returns error
deseq2 rlog
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
votes
0
replies
1.2k
views
taxonomy download from NCBI based on geneID
biomartr Bioconducter
6.5 years ago Jitendra ▴ 10
1
vote
2
replies
1.4k
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
2
votes
3
replies
2.3k
views
"Integrative transcriptomics" reveal or reveals?
english language omics orthography
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 60
0
votes
7
replies
1.1k
views
DESeq2 analysis for low RNA input
deseq2
6.5 years ago capricygcapricyg ▴ 10
2
votes
3
replies
2.2k
views
RNAseq and heatmap
deseq2 RNA-seq Heatmap
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
1
vote
2
replies
2.6k
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 3.5 years ago by ▴ 10 • written 6.5 years ago by ▴ 10
1
vote
2
replies
1.3k
views
Random effects in DESeq2
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
6
replies
1.6k
views
DESeq2: Error when correcting batch effect
deseq2 batch effect
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
votes
5
replies
2.0k
views
DESeq2-result files (.csv): Is there a convention for the IDs (e.g. gene names if produced for genes)
deseq2 gene format
6.5 years ago miriam.mueller • 0
3
votes
7
replies
1.5k
views
Questions for ResultsNames() and the Contrast function
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
8
votes
1
reply
11k
views
What can I do if I only have TPM but not raw counts data?
deseq2
updated 6.5 years ago by ★ 13k • written 6.5 years ago by ▴ 30
5
votes
5
replies
6.3k
views
tximport transcript missing
deseq2 salmon tximport
6.5 years ago mr6518849 ▴ 10
0
votes
4
replies
933
views
DESeq2 nested effect with 5 variables
deseq2 RNA-seq
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
votes
1
reply
3.3k
views
writing gse series matrix data into a csv file
R
6.5 years ago cs18s003 • 0
0
votes
0
replies
735
views
Why extractList fails to relist paired-end RNA-seq data when using pcoverageByTranscript?
GenomicAlignments pakcage extractList
6.6 years ago • updated 6.5 years ago Jiping Wang ▴ 90
1
vote
4
replies
3.1k
views
BiocParallel: What its the best way to pass large a dataset for parallel processing?
bioconductor bplapply bpiterate iterator BiocParallel
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 170
4
votes
2
replies
1.4k
views
Two-way interaction, linear redundancy
limma caret lm lmer lme4
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 110
4
votes
4
replies
3.8k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 670
4
votes
4
replies
1.4k
views
normalization of RNA-seq data after over-expressing the transcription factors
limma deseq2 voom edgeR
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 670
0
votes
2
replies
1.7k
views
Issue with xml files downloaded with `pathview()`
pathview kegg xml
updated 6.5 years ago by ★ 1.6k • written 6.6 years ago by ▴ 10
3
votes
2
replies
1.5k
views
Limma linear fit residual standard deviation calculation
limma
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 40
0
votes
1
reply
1.2k
views
How to center data points on coordinates (bases) in Gviz?
Gviz
6.5 years ago Robert ▴ 10
1
vote
2
replies
1.1k
views
Disagreement between results of two 'getBM' queries
BiomaRt biomart
6.5 years ago matrs ▴ 10
0
votes
1
reply
834
views
Incorrect DESeq2 Output
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
3
votes
10
replies
9.3k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
6.6 years ago • updated 6.5 years ago Robert ▴ 10
0
votes
6
replies
1.5k
views
DESeq2: Contrasts in multifactor design with interaction terms
r deseq2
6.5 years ago arielle • 0
0
votes
2
replies
1.5k
views
Contrast vs relevel (DESEq2)
deseq2 RNAseq
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
votes
3
replies
3.0k
views
DESeq2 more than 2 groups comparison
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
votes
3
replies
1.3k
views
collapseReplicates changes the order of the original dataframe in DESeq2
deseq2 collapseReplicates
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
8
votes
4
replies
5.7k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 670
0
votes
7
replies
6.1k
views
DEseq2 ncol(countData) == nrow(colData) is not TRUE Error
deseq2
6.5 years ago trumbia • 0
4
votes
3
replies
25k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 6.5 years ago by 53k • written 7.2 years ago by • 0
0
votes
4
replies
3.7k
views
deseq2 correction batch effect without design
deseq2 batch effect
updated 6.5 years ago by ★ 1.4k • written 6.5 years ago by • 0
46,742 results • Page 203 of 935
Recent ...
Replies
Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA by A.Barden ▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available by Tikaaa2sahaaaq2c • 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
Awards • All
Teacher to Michael Love 43k
Supporter to fl ▴ 20
Popular Question to James W. MacDonald 68k
Popular Question to rcavalca ▴ 140
Popular Question to James Aiden • 0
Locations • All
India, just now
United States, 31 minutes ago
Germany, 36 minutes ago
United States, 51 minutes ago
The city by the bay, 1 hour ago
Traffic: 1356 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