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Rank
Views
Votes
41
votes
44
replies
13k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR
p-value
DESeq
RNA-Seq
updated 7.4 years ago by
Wade Davis
▴ 60 • written 8.0 years ago by
yjiangnan
▴ 10
7
votes
44
replies
7.2k
views
OrgDB download failed via AnnotationHub
annotationhub
orgdb
updated 5.8 years ago by
shepherl
4.1k • written 5.9 years ago by
chirag.parsania
▴ 10
0
votes
44
replies
5.0k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 11 months ago by
Michael Love
43k • written 2.2 years ago by
Poonam
• 0
28
votes
43
replies
9.9k
views
Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
findoverlaps
granges
updated 9.0 years ago by
Martin Morgan
25k • written 9.2 years ago by
Jurat Shahidin
▴ 80
10
votes
41
replies
8.4k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 11 months ago by
Daniele
• 0 • written 6.4 years ago by
Guido Hooiveld
★ 4.1k
16
votes
40
replies
11k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 3.3 years ago by
Clara
▴ 10 • written 5.8 years ago by
lim6432
▴ 50
0
votes
38
replies
5.0k
views
running off target analaysis
crisprseek
8.2 years ago
Yap-JM
• 0
9
votes
38
replies
9.2k
views
manipulate bedpe format files
GRanges
bedpe
structural variants
rtracklayer
written 9.2 years ago by
tangming2005
▴ 200
25
votes
37
replies
13k
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 8.3 years ago by
Gordon Smyth
52k • written 8.3 years ago by
svlachavas
▴ 840
18
votes
37
replies
18k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma
illumina
differential gene expression
multiple comparisons
design matrix
9.9 years ago • updated 9.8 years ago
svlachavas
▴ 840
13
votes
35
replies
18k
views
RDAVIDWebService Error 301: Moved Permanently
rdavidwebservice
david
updated 6.8 years ago by
gevermalc
• 0 • written 9.8 years ago by
Vivek.b
▴ 100
0
votes
34
replies
11k
views
Error: installation of package org.Mm.eg.db had non-zero exit status
OrgDb
updated 5.0 years ago by
Michaël Degaud
• 0 • written 5.5 years ago by
zhangdengwei
• 0
1
vote
34
replies
5.1k
views
how to check which probesets belong to which transcript?
xps
affymetrix microarrays
humangene2.0ST
micro array data
updated 9.0 years ago by
cstrato
★ 3.9k • written 9.1 years ago by
Biologist
▴ 120
21
votes
34
replies
11k
views
Biomart error when updating to R 4.0.2
Biomart
updated 4.6 years ago by
Mike Smith
★ 6.6k • written 4.6 years ago by
landenshanie
▴ 40
1
vote
33
replies
5.4k
views
minfi failed positions in EPIC array
minfi
illuminahumanmethylationepicanno.ilmn10b.hg19
8.8 years ago
Giovanni Calice
▴ 160
8
votes
33
replies
5.0k
views
Unable to download hg19.generanges as part of DMRcatedata package
DMRacte
DMRcateranges
ExperimentHub
hg19.generanges
updated 4.3 years ago by
friedmanhiccc
▴ 10 • written 4.6 years ago by
richardallenfriedmanbrooklyn
▴ 30
0
votes
33
replies
3.7k
views
Wow, what have I done
updated 17.4 years ago by
Marcus G. Daniels
▴ 30 • written 17.4 years ago by
Loren Engrav
★ 1.0k
12
votes
33
replies
39k
views
Cannot install packages by BiocManager::install()
BiocManager
updated 3.0 years ago by
James W. MacDonald
68k • written 4.0 years ago by
mizzle
▴ 60
0
votes
32
replies
5.0k
views
Identify repetitive sequences in 10kbp promoter region in Mouse
granges
short tandem repetitions
repeat
8.3 years ago • updated 8.2 years ago
mkmb2004
• 0
2
votes
32
replies
6.1k
views
Gviz error 'Expectation Failed'
gviz
ucsc
8.9 years ago • updated 8.8 years ago
Tom
▴ 10
0
votes
32
replies
5.2k
views
How to do clustering
updated 17.9 years ago by
Seth Falcon
★ 7.4k • written 17.9 years ago by
ssls sddd
▴ 260
9
votes
32
replies
8.3k
views
Rsamtools v 1.99.6 installation error
Rsamtools
BiocManager
R 3.6
ubuntu
updated 6.0 years ago by
Hervé Pagès
16k • written 6.0 years ago by
kubovcij
• 0
0
votes
31
replies
5.3k
views
Error in find DEXSeq package
deseq
dexseq
10.0 years ago
engr.yahya602
• 0
8
votes
31
replies
5.5k
views
derfinder: analyzeChr() breaks on chromosomes > 22
derfinder
10.5 years ago
jessica.hekman
▴ 40
2
votes
30
replies
5.3k
views
ggbio 1.12.0 autoplot() with txdb example is broken
TranscriptDb
TranscriptDb
updated 11.0 years ago by
Tengfei Yin
▴ 490 • written 11.0 years ago by
Leonardo Collado Torres
★ 1.1k
2
votes
30
replies
5.0k
views
create design matrix when 2 groups of gene-expression data
limma
9.3 years ago • updated 9.0 years ago
mheydarpour
▴ 10
5
votes
30
replies
5.9k
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 29 days ago by
wuwenhui2
• 0 • written 7.8 years ago by
heikki.sarin
▴ 10
34
votes
29
replies
16k
views
[DESeq2] time series strain-specific differences over time
deseq2
timecourse
updated 7 months ago by
Michael Love
43k • written 10.1 years ago by
john
▴ 130
44
votes
29
replies
13k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db
pathview
updated 4.0 years ago by
Kevin Ushey
▴ 130 • written 4.1 years ago by
Arun
▴ 160
0
votes
28
replies
3.3k
views
countMatches() (was: table for GenomicRanges)
Cancer
IRanges
Cancer
IRanges
updated 12.3 years ago by
Michael Lawrence
★ 11k • written 12.3 years ago by
Hervé Pagès
16k
2
votes
28
replies
6.3k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub
AnnotationForge
Pseudomonas_aeruginosa
updated 17 months ago by
James W. MacDonald
68k • written 2.4 years ago by
Manmohit
▴ 10
7
votes
28
replies
7.7k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 15 months ago by
Gordon Smyth
52k • written 10.1 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
28
replies
4.1k
views
Job:
Postdoc on integrating and analyzing new transcriptome types in the Bgee database
rnaseq
data integration
single-cell
pacbio
across species
Job
7.1 years ago
bgee
• 0
0
votes
27
replies
3.5k
views
summarizeOverlaps mode ignoring inter feature overlaps
12.1 years ago
Thomas Girke
★ 1.7k
4
votes
27
replies
4.9k
views
FourCseq - error countFragmentOverlaps()
FourCseq
fourcseq
updated 9.9 years ago by
ericaenjoy3
• 0 • written 9.9 years ago by
Theo
▴ 10
2
votes
27
replies
5.1k
views
CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for regions < 200kb
crisprseek
sgrna
crispr
cas9
R
9.6 years ago • updated 9.5 years ago
alexgraehl
▴ 20
2
votes
27
replies
3.1k
views
Applying NetAffx biological annotation to Affymetrix gene expression dataset
microarray
annotation
updated 6.1 years ago by
James W. MacDonald
68k • written 6.1 years ago by
lm795
▴ 10
1
vote
26
replies
7.7k
views
How can I install DeSeq2 in Jupyter Notebook?
deseq2
updated 6.2 years ago by
Marc Saric
▴ 70 • written 6.2 years ago by
david.wheeler7
▴ 20
3
votes
26
replies
5.3k
views
How to prepare targets.txt file in codelink.
r
codelink
updated 10.0 years ago by
Diego Diez
▴ 760 • written 10.0 years ago by
Agaz Hussain Wani
▴ 260
0
votes
25
replies
3.6k
views
deseq2 course experiment
deseq2
7.9 years ago
ribioinfo
▴ 100
11
votes
25
replies
12k
views
readCufflinks problem with extdata
cummerbund
updated 7.6 years ago by
markus.ball
▴ 10 • written 7.8 years ago by
biakemi
▴ 40
5
votes
25
replies
2.4k
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 13 months ago by
Gordon Smyth
52k • written 13 months ago by
Jitendra
▴ 10
1
vote
25
replies
5.2k
views
DiffBind spike-in normalization
DiffBind
2.5 years ago
yuhuihui2011
• 0
28
votes
25
replies
6.7k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz
rtracklayer
updated 7.8 years ago by
aina.jene
▴ 10 • written 8.2 years ago by
Ramiro Magno
▴ 100
2
votes
25
replies
7.6k
views
How to use Limma to analyze differences among group items without doing pairwise comparisons
limma
9.0 years ago • updated 8.9 years ago
sami.pietila
• 0
16
votes
25
replies
4.2k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 6.1 years ago by
fiona.dick91
▴ 60
6
votes
25
replies
4.2k
views
How to import normalized file (using xps) to limma for differential expressed genes?
xps
heatmap
limma
updated 9.1 years ago by
cstrato
★ 3.9k • written 9.1 years ago by
Biologist
▴ 120
21
votes
24
replies
14k
views
Problem with biomart's listMarts function
biomart
bug
updated 9.0 years ago by
Paul Shannon
▴ 470 • written 9.5 years ago by
Johannes Rainer
★ 2.1k
3
votes
24
replies
4.3k
views
Problem in installing maEndToEnd package
microarray
maEndToEnd
5.7 years ago • updated 5.6 years ago
Jack
• 0
1
vote
24
replies
6.2k
views
GenomicAlignments - extracting sequence signatures from bam file
bam file
HIV
cytosine
7.6 years ago
achaillon
• 0
46,470 results • Page
1 of 930
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Replies
Comment: Cannot extract size factor from DESeq2 analysis
by
s.malik
• 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function
by
Vishnu
• 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2
by
Tom
• 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function
by
ATpoint
★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq
by
caroline.zanchi
• 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Votes
Comment: Filtering after DESeq
A: Normalized counts from DESeq2 results in similar but not equal total read count?
A: DESeq2: Different Dispersions for different sample groups
A: Contrasts & coefficients in limma
Answer: How to formulate 2 factor nested design in DESeq2
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