2
votes
3
replies
3.7k
views
How to remove aberrant chromosomes from a BSgenome object?
bsgenome r
updated 9.6 years ago by 16k • written 9.6 years ago by • 0
5
votes
6
replies
2.8k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
9.6 years ago saadmurtazakhan ▴ 10
0
votes
0
replies
1.0k
views
Data adjustment requirements for input in time-course BETR analysis
betr timecourse
9.6 years ago Quang Nguyen • 0
1
vote
1
reply
1.3k
views
limma for shRNA dropout screen analysis?
limma gmap shRNA dropout screen
updated 9.6 years ago by ★ 29k • written 9.6 years ago by ▴ 40
1
vote
5
replies
2.2k
views
DECIPHER version bug using biocLite()
DECIPHER
9.6 years ago Vinicius Henrique da Silva ▴ 40
0
votes
4
replies
2.3k
views
Error when launching shiny app in cytofkit
cytofkit
updated 9.6 years ago by ▴ 30 • written 9.6 years ago by ▴ 10
5
votes
15
replies
4.6k
views
nearest genes using TxDb.Hsapiens.UCSC.hg19
txdb.hsapiens.ucsc.hg19.knowngene ChIPpeakAnno
updated 9.6 years ago by ★ 4.3k • written 9.6 years ago by ▴ 140
2
votes
2
replies
1.3k
views
EdgeR-type analysis for ranked data?
EdgeR rank
9.6 years ago knaxerova ▴ 10
0
votes
0
replies
1.2k
views
Analysis of MBD-seq data without ssl control using BayMeth
Baymeth methylation MBD-seq Repitools
9.6 years ago pm2015 • 0
0
votes
6
replies
2.4k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2 chip-seq Differential binding
9.6 years ago p2016k • 0
2
votes
6
replies
2.0k
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de contrast design and contrast matrix
updated 9.6 years ago by ★ 29k • written 9.6 years ago by ▴ 300
0
votes
3
replies
2.5k
views
Newer version of DESeq2 gives different results
deseq2 phyloseq
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
1
vote
3
replies
2.2k
views
DESeq2 with paired data Heatmap
deseq2 heatmap
updated 9.6 years ago by ★ 13k • written 9.6 years ago by • 0
2
votes
2
replies
1.6k
views
Cannot load old SummarizedExperiment in R 3.3, Bioc 3.3
summarizedexperiment backwards compatibility
updated 9.6 years ago by 16k • written 9.6 years ago by ★ 7.9k
1
vote
2
replies
1.3k
views
edgeR for CNV detection
edgeR
updated 9.6 years ago by ★ 7.9k • written 9.6 years ago by ▴ 160
6
votes
4
replies
4.9k
views
How to generate a PCA scree plot in DESeq2?
pca deseq2 PCA scree plot
9.6 years ago CandiceChuDVM ▴ 40
0
votes
3
replies
1.3k
views
DESeq2 with paired data
deseq
9.6 years ago l.weissenburgermoser • 0
0
votes
1
reply
1.6k
views
Questions for MEDIPS getPairedGRange function in MEDIPS.readRegionsFile.R
medips bam file
9.6 years ago fkuo ▴ 10
1
vote
0
replies
1.5k
views
Error when computing ld with snpStats in big samples
software error snpstats `ld
9.6 years ago carlos.ruiz • 0
0
votes
0
replies
1.8k
views
"error: C stack usage 265532545 is too close to the limit" with running ChAMP
ChAMP
9.6 years ago chaoqiang.lai • 0
0
votes
0
replies
1.3k
views
News: Announcement of a new package called bacon
software r News
9.6 years ago m.van_iterson ▴ 20
0
votes
1
reply
4.4k
views
normalized FPKM counts from DEseq2
deseq2
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
1
vote
4
replies
1.4k
views
Can DESEQ2 be used to determine DE from targeted RNA-Seq?
deseq2
9.6 years ago Seanna.McTaggart • 0
6
votes
2
replies
5.5k
views
How to get the intersect and get the difference of a grange object while keeping meta data
genomicranges intersect
updated 9.6 years ago by 4.2k • written 9.7 years ago by ▴ 30
15
votes
4
replies
13k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 3.8 years ago by 16k • written 9.6 years ago by ▴ 40
1
vote
0
replies
2.5k
views
Job: Bioinformatics Scientist @ Berlin Institute for Medical Systems Biology
rnaseq snp chipseq Job
9.6 years ago altuna akalin ▴ 20
0
votes
2
replies
3.6k
views
Use surrogate variables on DESeq2
deseq2 sva deseq differential gene expression
updated 9.6 years ago by ▴ 20 • written 10.4 years ago by ▴ 40
2
votes
3
replies
2.0k
views
RNAseq outlier is a critical sample
rnaseq outlier statistics batch effect
updated 9.6 years ago by 53k • written 9.6 years ago by • 0
1
vote
2
replies
2.2k
views
edgeR | paired samples | multiple baseline | averaging baseline or not
edger rnaseq baseline linear model negative binomial model
updated 9.6 years ago by 53k • written 9.8 years ago by • 0
0
votes
2
replies
2.2k
views
Subsetting info columns from a VCF and getting rsID for some row names?
R variantannotation vcf scanvcfparam readvcf
updated 9.6 years ago by ★ 11k • written 9.6 years ago by • 0
7
votes
19
replies
20k
views
Can't load package "org.Hs.eg.db"
org.Hs.eg.db
updated 4.5 years ago by • 0 • written 10.3 years ago by ▴ 40
0
votes
1
reply
1.1k
views
Iteration through a list failing
geoquery
updated 9.6 years ago by 68k • written 9.6 years ago by • 0
0
votes
0
replies
1.6k
views
Running Mclust package in R, using maximum a posteriori (MAP)
r mclust clustering
9.6 years ago mabdulsa • 0
14
votes
16
replies
3.8k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma toptable
9.6 years ago giroudpaul ▴ 40
0
votes
3
replies
1.7k
views
plotting coverage in log scale with Gviz
Gviz gviz
9.6 years ago Alejandro Reyes ★ 1.9k
4
votes
1
reply
881
views
How to fit a regression for a time series array experiment with limma?
limma microarray
updated 9.6 years ago by 68k • written 9.6 years ago by ▴ 420
0
votes
7
replies
2.4k
views
Error in loading rsbml
rsbml BiGGR
9.6 years ago enrico.moiso • 0
1
vote
1
reply
1.8k
views
install IlluminaHumanMethylation450k.db error
illuminahumanmethylation450k.db
updated 9.6 years ago by 25k • written 9.6 years ago by ▴ 200
1
vote
1
reply
4.1k
views
Read.table: Skip Column
read.table
updated 9.6 years ago by 25k • written 9.6 years ago by • 0
0
votes
1
reply
1.9k
views
ChIPseeker gene body plot
chipseeker visualization
updated 9.6 years ago by ★ 1.2k • written 9.6 years ago by ▴ 50
0
votes
1
reply
1.3k
views
ExpressionSet: Internal Standard
expressionset
updated 9.6 years ago by ★ 13k • written 9.6 years ago by • 0
2
votes
2
replies
2.7k
views
Can I calculate counts from the base mean and log2fc outputs of DESeq2? Also, can I calculate error for counts values from lfcse output?
deseq2 chipseq counts log2fc error
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
2
votes
2
replies
1.7k
views
Running Roast with Gene Symbols of Curated Genes
mroast roast gene set gene set analysis edgeR
updated 9.6 years ago by 68k • written 9.6 years ago by • 0
1
vote
5
replies
2.6k
views
Making package compatible with old version of R/Bioconductor
bioconductor R software error biocinstaller
9.6 years ago gabriel.hoffman ▴ 170
2
votes
2
replies
2.2k
views
How to : Preprocessing of Gene ST array with Oligo
oligo hugene20st
updated 9.6 years ago by 68k • written 9.6 years ago by ▴ 40
3
votes
4
replies
1.8k
views
design matrix - control for biological replicates
limma
9.6 years ago map2085 ▴ 40
6
votes
18
replies
4.6k
views
biomaRt - getBM - biomart= ENSEMBL_MART_FUNCGEN !!! NOT WORKING!!!
bioconductor biomart problem with connection
updated 9.6 years ago by ▴ 70 • written 9.6 years ago by ▴ 10
3
votes
1
reply
1.6k
views
how duplicates reads would affect Differential expression analysis results
limma differential gene expression bioconductor
updated 9.6 years ago by ★ 29k • written 9.6 years ago by • 0
1
vote
2
replies
932
views
Best approach to analyse this time series experiment
microarray
updated 9.6 years ago by 53k • written 9.6 years ago by ▴ 420
1
vote
1
reply
1.1k
views
challenging design matrix
limma design matrix differential gene expression limma
updated 9.6 years ago by 53k • written 9.6 years ago by • 0
46,704 results • Page 391 of 935
Recent ...
Replies
Answer: How to do differential expresion across time serise with edgeR? by Gordon Smyth 53k
One obvious issue is that you are conducting an old-style edgeR v2 LRT test instead of using the newer edgeR v4 QL pipeline designed to dea…
Answer: ATACseq rudimentary questions by Kevin Blighe ★ 4.0k
For differential analysis tools like DiffTF and TOBIAS, the standard and statistically sound approach is to create **one large consensus pe…
Answer: How to install packages such as TCGAbiolinks, SumarizedExperiment? by Gordon Smyth 53k
The warning message is telling you that you already have the packages installed. However, you might consider upgrading to the current vers…
Comment: Empty boxes in treemap plot rrvgo package by TikTsokaasocissalpc • 0
Clear visualization matters just as much in mobile entertainment as in data analysis. The [Try KK33 Game App now][1] focuses on clean layou…
Comment: nice 3D displays for PCA analysis by adam80haynes • 0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Votes
Answer: How to install packages such as TCGAbiolinks, SumarizedExperiment?
A: limma-voom duplicateCorrelation once or twice, difference?
A: limma: comparison of repeat measurements - blocking or within-subject correlatio
Answer: DecideTest vs topTAGs in edgeR
A: LIMMA time series spline model.matrix design setup
Awards • All
Popular Question to ZheFrench ▴ 60
Teacher to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Popular Question to Hervé Pagès 16k
Popular Question to Vincent J. Carey, Jr. 6.7k
Locations • All
WEHI, Melbourne, Australia, 11 minutes ago
Denmark, 15 minutes ago
United Kingdom, 28 minutes ago
Seattle, WA, United States, 1 hour ago
The Cave, 181 Longwood Avenue, Boston, USA, 3 hours ago
Traffic: 1055 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