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Views
Votes
41
votes
44
replies
10k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR
p-value
DESeq
RNA-Seq
updated 6.4 years ago by
Wade Davis
▴ 60 • written 7.0 years ago by
yjiangnan
▴ 10
7
votes
44
replies
5.4k
views
OrgDB download failed via AnnotationHub
annotationhub
orgdb
updated 4.8 years ago by
shepherl
3.9k • written 4.9 years ago by
chirag.parsania
• 0
28
votes
43
replies
8.5k
views
Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
findoverlaps
granges
updated 8.1 years ago by
Martin Morgan
25k • written 8.2 years ago by
Jurat Shahidin
▴ 80
16
votes
40
replies
8.6k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 2.3 years ago by
Clara
• 0 • written 4.8 years ago by
lim6432
▴ 50
9
votes
38
replies
6.8k
views
manipulate bedpe format files
GRanges
bedpe
structural variants
rtracklayer
written 8.2 years ago by
tangming2005
▴ 190
0
votes
38
replies
3.5k
views
running off target analaysis
crisprseek
7.2 years ago
Yap-JM
• 0
25
votes
37
replies
11k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq
RSEM
TCGA
edgeR
normalization
updated 7.3 years ago by
Gordon Smyth
50k • written 7.3 years ago by
svlachavas
▴ 830
18
votes
37
replies
17k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma
illumina
differential gene expression
multiple comparisons
design matrix
8.9 years ago • updated 8.8 years ago
svlachavas
▴ 830
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 4 weeks ago by
Shiva
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 3.9k
13
votes
35
replies
16k
views
RDAVIDWebService Error 301: Moved Permanently
rdavidwebservice
david
updated 5.8 years ago by
gevermalc
• 0 • written 8.8 years ago by
Vivek.b
▴ 100
21
votes
34
replies
8.4k
views
Biomart error when updating to R 4.0.2
Biomart
updated 3.6 years ago by
Mike Smith
★ 6.5k • written 3.6 years ago by
landenshanie
▴ 40
1
vote
34
replies
3.8k
views
how to check which probesets belong to which transcript?
xps
affymetrix microarrays
humangene2.0ST
micro array data
updated 8.1 years ago by
cstrato
★ 3.9k • written 8.1 years ago by
Biologist
▴ 110
0
votes
34
replies
8.4k
views
Error: installation of package org.Mm.eg.db had non-zero exit status
OrgDb
updated 4.1 years ago by
Michaël Degaud
• 0 • written 4.5 years ago by
zhangdengwei
• 0
1
vote
33
replies
4.1k
views
minfi failed positions in EPIC array
minfi
illuminahumanmethylationepicanno.ilmn10b.hg19
7.9 years ago • updated 7.8 years ago
Giovanni Calice
▴ 160
0
votes
33
replies
2.7k
views
Wow, what have I done
updated 16.4 years ago by
Marcus G. Daniels
▴ 30 • written 16.4 years ago by
Loren Engrav
★ 1.0k
8
votes
33
replies
3.7k
views
Unable to download hg19.generanges as part of DMRcatedata package
DMRacte
DMRcateranges
ExperimentHub
hg19.generanges
updated 3.3 years ago by
friedmanhiccc
▴ 10 • written 3.7 years ago by
richardallenfriedmanbrooklyn
▴ 20
12
votes
33
replies
28k
views
Cannot install packages by BiocManager::install()
BiocManager
updated 2.0 years ago by
James W. MacDonald
65k • written 3.0 years ago by
mizzle
▴ 60
9
votes
32
replies
6.0k
views
Rsamtools v 1.99.6 installation error
Rsamtools
BiocManager
R 3.6
ubuntu
updated 5.0 years ago by
Hervé Pagès
16k • written 5.0 years ago by
kubovcij
• 0
0
votes
32
replies
4.0k
views
How to do clustering
updated 16.9 years ago by
Seth Falcon
★ 7.4k • written 16.9 years ago by
ssls sddd
▴ 260
2
votes
32
replies
4.9k
views
Gviz error 'Expectation Failed'
gviz
ucsc
7.9 years ago • updated 7.8 years ago
Tom
▴ 10
0
votes
32
replies
3.8k
views
Identify repetitive sequences in 10kbp promoter region in Mouse
granges
short tandem repetitions
repeat
7.3 years ago • updated 7.2 years ago
mkmb2004
• 0
0
votes
31
replies
4.3k
views
Error in find DEXSeq package
deseq
dexseq
9.0 years ago
engr.yahya602
• 0
8
votes
31
replies
4.4k
views
derfinder: analyzeChr() breaks on chromosomes > 22
derfinder
9.5 years ago
jessica.hekman
▴ 40
2
votes
30
replies
4.3k
views
ggbio 1.12.0 autoplot() with txdb example is broken
TranscriptDb
TranscriptDb
updated 10.0 years ago by
Tengfei Yin
▴ 490 • written 10.0 years ago by
Leonardo Collado Torres
★ 1.0k
2
votes
30
replies
4.1k
views
create design matrix when 2 groups of gene-expression data
limma
8.3 years ago • updated 8.0 years ago
mheydarpour
▴ 10
0
votes
29
replies
2.4k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 6 hours ago by
Michael Love
41k • written 15 months ago by
Poonam
• 0
44
votes
29
replies
11k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db
pathview
updated 3.0 years ago by
Kevin Ushey
▴ 130 • written 3.1 years ago by
Arun
▴ 160
0
votes
28
replies
2.5k
views
countMatches() (was: table for GenomicRanges)
Cancer
IRanges
Cancer
IRanges
updated 11.3 years ago by
Michael Lawrence
★ 11k • written 11.3 years ago by
Hervé Pagès
16k
7
votes
28
replies
6.2k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 3 months ago by
Gordon Smyth
50k • written 9.2 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
28
replies
3.2k
views
Job:
Postdoc on integrating and analyzing new transcriptome types in the Bgee database
rnaseq
data integration
single-cell
pacbio
across species
Job
6.1 years ago
bgee
• 0
2
votes
28
replies
4.4k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub
AnnotationForge
Pseudomonas_aeruginosa
updated 5 months ago by
James W. MacDonald
65k • written 17 months ago by
Manmohit
▴ 10
0
votes
27
replies
2.8k
views
summarizeOverlaps mode ignoring inter feature overlaps
11.1 years ago
Thomas Girke
★ 1.7k
4
votes
27
replies
3.8k
views
FourCseq - error countFragmentOverlaps()
FourCseq
fourcseq
updated 8.9 years ago by
ericaenjoy3
• 0 • written 8.9 years ago by
Theo
▴ 10
2
votes
27
replies
4.0k
views
CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for regions < 200kb
crisprseek
sgrna
crispr
cas9
R
8.6 years ago • updated 8.5 years ago
alexgraehl
▴ 20
5
votes
27
replies
3.7k
views
DESeq2 model - How to test case/control time course model when taking account within sample variability?
deseq2
multiple time points
time course
casecontrol
model design
updated 3.4 years ago by
Michael Love
41k • written 6.8 years ago by
heikki.sarin
▴ 10
2
votes
27
replies
2.1k
views
Applying NetAffx biological annotation to Affymetrix gene expression dataset
microarray
annotation
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
lm795
▴ 10
3
votes
26
replies
4.4k
views
How to prepare targets.txt file in codelink.
r
codelink
updated 9.0 years ago by
Diego Diez
▴ 760 • written 9.1 years ago by
Agaz Hussain Wani
▴ 260
1
vote
26
replies
6.1k
views
How can I install DeSeq2 in Jupyter Notebook?
deseq2
updated 5.2 years ago by
Marc Saric
▴ 70 • written 5.2 years ago by
david.wheeler7
▴ 20
0
votes
25
replies
2.8k
views
deseq2 course experiment
deseq2
7.0 years ago • updated 6.9 years ago
ribioinfo
▴ 100
11
votes
25
replies
11k
views
readCufflinks problem with extdata
cummerbund
updated 6.6 years ago by
markus.ball
▴ 10 • written 6.9 years ago by
biakemi
▴ 40
1
vote
25
replies
3.4k
views
DiffBind spike-in normalization
DiffBind
19 months ago • updated 18 months ago
yuhuihui2011
• 0
28
votes
25
replies
5.9k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz
rtracklayer
updated 6.8 years ago by
aina.jene
▴ 10 • written 7.2 years ago by
Ramiro Magno
▴ 100
2
votes
25
replies
6.2k
views
How to use Limma to analyze differences among group items without doing pairwise comparisons
limma
8.0 years ago
sami.pietila
• 0
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.1 years ago by
fiona.dick91
▴ 60
5
votes
25
replies
935
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
6
votes
25
replies
3.2k
views
How to import normalized file (using xps) to limma for differential expressed genes?
xps
heatmap
limma
updated 8.1 years ago by
cstrato
★ 3.9k • written 8.1 years ago by
Biologist
▴ 110
21
votes
24
replies
13k
views
Problem with biomart's listMarts function
biomart
bug
updated 8.0 years ago by
Paul Shannon
▴ 470 • written 8.5 years ago by
Johannes Rainer
★ 2.0k
0
votes
24
replies
3.0k
views
Error in QAReport function of package affyQCReport
affy
affy
updated 16.8 years ago by
Seth Falcon
★ 7.4k • written 16.8 years ago by
Mark W Kimpel
▴ 830
5
votes
24
replies
3.4k
views
CRISPRseek scoring clarification
crisprseek
updated 6.5 years ago by
Julie Zhu
★ 4.3k • written 7.2 years ago by
elspeth.ransom
• 0
1
vote
24
replies
4.8k
views
GenomicAlignments - extracting sequence signatures from bam file
bam file
HIV
cytosine
6.6 years ago
achaillon
• 0
45,619 results • Page
1 of 913
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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