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0
votes
0
replies
1.2k
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Vertically Flipped Sashimi Plot
Gviz
Sashimi Plot
8.6 years ago
Dario Strbenac
★ 1.6k
3
votes
4
replies
2.0k
views
No annotation for single SNPs
variantannotation
SNPs
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
updated 8.6 years ago by
Valerie Obenchain
★ 6.8k • written 8.6 years ago by
Lna
• 0
1
vote
3
replies
1.5k
views
extracting cluster data after using flowpeaks
flowpeaks
8.6 years ago
shadhiksk
• 0
4
votes
3
replies
1.9k
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 8.6 years ago by
Ou, Jianhong
★ 1.3k • written 8.6 years ago by
Haiying.Kong
▴ 110
2
votes
6
replies
2.5k
views
DESeq2 Dispersion Estimation after Applying Customized Normalization Factors
deseq2
8.6 years ago
dustar1986
▴ 10
1
vote
1
reply
4.7k
views
edgeR reinstall failure: edgeR.rdb' is corrupt
edgeR
package installation
updated 8.6 years ago by
Aaron Lun
★ 29k • written 8.6 years ago by
afreedman405
• 0
0
votes
8
replies
3.9k
views
Does fgsea order the stats argument?
fgsea
8.6 years ago
rubi
▴ 110
1
vote
2
replies
2.3k
views
drawing chemical from smile 2D/3D
chemminer
updated 8.6 years ago by
Thomas Girke
★ 1.7k • written 8.6 years ago by
Stane
▴ 40
0
votes
6
replies
3.9k
views
KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
kegggraph
8.6 years ago
AR3513
• 0
3
votes
3
replies
2.1k
views
question about subsetting SGSeq results by different categories of splice events
sgseq
updated 8.6 years ago by
Leonard Goldstein
▴ 260 • written 8.6 years ago by
amanda.joy.price
▴ 10
0
votes
3
replies
1.2k
views
how to apply correctly geneSetTest on deseq2 data results
deseq2
limma
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
jarod_v6@libero.it
▴ 40
1
vote
8
replies
8.0k
views
How to perform DESeq2 based on paired sample test?
rnaseq
deseq2
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
zhxiaokang
▴ 20
7
votes
8
replies
2.2k
views
limma: same data in different formats produces different DEG-analysis results
limma
8.6 years ago
littlefishes20
▴ 10
2
votes
4
replies
1.5k
views
package "isa2", function isa.iterate()
source code
isa.iterate()
updated 8.6 years ago by
Haiying.Kong
▴ 110 • written 8.6 years ago by
zhang.jianhai
▴ 10
0
votes
3
replies
2.6k
views
error in champ.DMR using DMRcate (v2.8.3)
champ
dmrcate
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
updated 8.6 years ago by
Yuan Tian
▴ 90 • written 8.6 years ago by
mia
• 0
1
vote
0
replies
1.5k
views
Gviz failed to fetch ideogram information from UCSC
gviz
8.6 years ago
izzy.yichao.cai
▴ 10
0
votes
2
replies
1.3k
views
R package help
r package problem
8.6 years ago
Mohamad S. Hasan
• 0
1
vote
1
reply
6.7k
views
DESeq2 with continuous variables - predictors and/or outcomes
deseq2
negative binomial model
robust regression
sleuth
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
stoyo_karamihalev
• 0
0
votes
3
replies
1.9k
views
Batch effects and model matrices
deseq2
single cell
monocle
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
bvernot
• 0
0
votes
10
replies
2.9k
views
behaviour of findOverlaps on GRangesList object
findOverlaps
grangeslist
GenomicRanges
8.6 years ago
lovro0
▴ 10
0
votes
0
replies
605
views
plotting gene expression correlation and gene distance
R
8.6 years ago
safy_abaza
• 0
1
vote
7
replies
2.6k
views
Ballgown object construction error
ballgown
scan
error
package
8.6 years ago
spaque57
• 0
0
votes
1
reply
2.4k
views
How to get treatment information with TCGAbiolinks?
gdcprepare
tcgabiolinks
treatment_type
R
data extraction
updated 8.6 years ago by
Dario Strbenac
★ 1.6k • written 8.6 years ago by
newbie
• 0
2
votes
3
replies
2.8k
views
Error in champ.load (v. 2.8.3)
champ
ChAMP
updated 8.6 years ago by
Yuan Tian
▴ 90 • written 8.6 years ago by
rasmus.rydbirk
▴ 10
0
votes
4
replies
1.5k
views
Rsamtools fetch MD:Z field from bam files
Rsamtools fetch MD:Z field from bam files
8.6 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
1.3k
views
r3Cseq problems in batch mode
r3Cseq
updated 8.6 years ago by
izzy.yichao.cai
▴ 10 • written 9.9 years ago by
manduchi
▴ 10
0
votes
6
replies
5.7k
views
How to perform ANOVA to calculate differential gene expression with three categories
anova
updated 8.6 years ago by
Gordon Smyth
53k • written 8.6 years ago by
pbachali
▴ 50
3
votes
2
replies
4.3k
views
Sparse matrices in Bioconductor objects for single-cell analyses
scater
simpleSingleCell
workflows
updated 8.6 years ago by
Aaron Lun
★ 29k • written 8.6 years ago by
sandmann.t
▴ 70
0
votes
2
replies
1.9k
views
Converting Exon counts(co-ordinates) to transcript/gene ids
dexseq
bioconductor
cancer
rna-seq
8.6 years ago
Shrule
• 0
2
votes
3
replies
2.1k
views
Sample not clustering as expected in DESeq2
deseq2
Euclidean sample distance
8.6 years ago
gkuffel
▴ 10
1
vote
3
replies
1.2k
views
Function Rf_lgammafn() in the log_posterior function in the DESeq2 C++ functions
deseq2
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
vtshen
• 0
0
votes
0
replies
1.2k
views
Error in readPlateList
cellhts2
error
8.6 years ago
sil1
• 0
0
votes
2
replies
4.1k
views
Error using TCGAbiolinks "Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column"
TCGA
tcgabiolinks
Error
8.6 years ago
f.geist
▴ 20
0
votes
2
replies
1.6k
views
getReadCountsFromBAM and paired-end reads
cn.mops
8.6 years ago
Alexandre Kuhn
▴ 20
4
votes
2
replies
2.0k
views
using cn.MOPS on WES data GERMLINE-TUMOR
cn.mops
8.6 years ago
Bogdan
▴ 670
1
vote
3
replies
1.4k
views
edgeR 4 conditions
edger
8.6 years ago
Paolo Kunderfranco
▴ 350
4
votes
2
replies
3.4k
views
GSVA: questions about the bootstrap p-value
gsva
updated 8.6 years ago by
Robert Castelo
★ 3.4k • written 8.6 years ago by
dionnezaal
▴ 30
0
votes
6
replies
3.2k
views
Error using readVcf
gwastools
variantannotation
updated 8.6 years ago by
Stephanie M. Gogarten
▴ 890 • written 8.6 years ago by
Lna
• 0
0
votes
1
reply
1.4k
views
DiffBind :Retrieve count value from Diffbind by dab.report
diffbind
updated 8.6 years ago by
Rory Stark
★ 5.2k • written 8.6 years ago by
JunLVI
▴ 40
0
votes
3
replies
1.3k
views
Diffbind: retrieve raw peaks per sample
diffbind
updated 8.6 years ago by
Rory Stark
★ 5.2k • written 8.6 years ago by
ZheFrench
▴ 60
0
votes
0
replies
1.1k
views
Discordant Differential Expression
ballgown
8.6 years ago
lindsaynhayes
• 0
0
votes
10
replies
2.0k
views
DESeq2: design - 1 ctl, 2 different treated
deseq2
8.6 years ago
charlesh
• 0
0
votes
1
reply
2.7k
views
how to use q value to select differentially expressed genes
rnaseq
updated 8.6 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.6 years ago by
ahmadvandra
• 0
0
votes
0
replies
1.1k
views
How to use clusterprofiler
R
8.6 years ago
nakanomasayuki265
• 0
0
votes
1
reply
2.0k
views
Chip-seq peak annotation [Chipseeker]
chipseeker
chip-seq
annotation
Guangchuang
updated 8.6 years ago by
Guangchuang Yu
★ 1.2k • written 8.6 years ago by
anupriyaverma1408
• 0
0
votes
1
reply
1.6k
views
Visualizing Linear Model Coefficients in R
R
deseq2
graph
linear model
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
nathanguy14
• 0
0
votes
6
replies
2.6k
views
Bam file analysis fro beginner
bioconductor
8.6 years ago
Morris
▴ 10
2
votes
2
replies
2.7k
views
DESeq2: Error: could not find function "vst"
deseq2
8.6 years ago
charlesh
• 0
0
votes
2
replies
1.9k
views
Subsetting clusters in flowPeaks
flowCore
flowViz
flowPeaks
flowCore
flowViz
flowPeaks
updated 8.6 years ago by
shadhiksk
• 0 • written 11.5 years ago by
Hefin Rhys Jones
▴ 30
0
votes
2
replies
2.8k
views
Exporting a GenomicRanges object as GTF/GFF file
genomicranges
rtracklayer
gtf
gff
export
8.6 years ago
rubi
▴ 110
46,729 results • Page
326 of 935
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Replies
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
You may want to look at the coefficients you are trying to estimate with ExploreModelMatrix: https://www.bioconductor.org/packages/relea…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
emily.wolfrum
• 0
Hi Gordon, Thanks for the quick reply. The technical or process blank samples I'm referring to are part of a set of quality control sampl…
Answer: Are individual-mouse-based statistics possible in CellChat?
by
ATpoint
★ 5.0k
Not a Bioconductor package, I commented on the crosspost at https://www.biostars.org/p/9617271/
Answer: DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
by
ATpoint
★ 5.0k
apeglm is more cumbersome than ashr as with apeglm the coefficients need to be explicitely available in the resultsNames.So, you need to re…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Martin Morgan
25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Votes
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
Answer: When to use edgeR or limma
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