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Votes
6
votes
5
replies
2.2k
views
t-statistic from various limma-approaches does not follow the theoretical distribution
limma
t-statistic
voom
voomwithqualityweights
robust regression
7.2 years ago
brynedal
▴ 40
2
votes
3
replies
2.7k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2
deseq
rnaseq
outliers
count outliers
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
lefeverde
▴ 10
0
votes
1
reply
2.7k
views
WGCNA: Matching eigengenes to samples
wgcna
wgcna package
7.2 years ago
Jack
• 0
0
votes
9
replies
3.9k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread
alignment
align
7.2 years ago
A
▴ 60
2
votes
1
reply
2.2k
views
Ensemble and Entrez disconnected?
ensembl
entrez
biomart
org.hs.eg.db
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
bettina.budeus
• 0
0
votes
3
replies
1.7k
views
Post-hoc filtering on the standard deviation in proportions
drimseq
rnaseqdtu
stager
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
Jack.Hearn
• 0
0
votes
4
replies
1.4k
views
DESeq2: Analyzing just two normal+tumour pairs
deseq2
reporting tools
7.2 years ago
mmokrejs
• 0
0
votes
1
reply
2.1k
views
ReportingTools: Error using packet 1 arguments must have same length
reportingtools
7.2 years ago
mmokrejs
• 0
1
vote
12
replies
7.1k
views
Install rtracklayer with the Error undefined symbol: OPENSSL_init_ssl (system Centos7.3 R3.5.1 openssl-1.1.1)
software error
rtracklayer
bioconductor
openssl
7.2 years ago
ruan_wei_dong
• 0
2
votes
2
replies
1.5k
views
Help for Research Proposal
drug development
pathways
bioinformatics
updated 7.2 years ago by
Steve Lianoglou
★ 13k • written 7.2 years ago by
wajeehaejaz17
• 0
1
vote
2
replies
2.1k
views
ggbio won't plot ideogram in R version 3.3.1, ggplot2 version 3.1.0
ggbio
ggplot2
7.2 years ago
t.fadason
▴ 10
2
votes
2
replies
1.7k
views
edgeR DE analysis: single group combined factors or GLM with interaction term
edger
glm
updated 7.2 years ago by
Aaron Lun
★ 29k • written 7.2 years ago by
jspmccain
▴ 10
1
vote
1
reply
840
views
how to retrieve gene id from topGO results
rnaseq
7.2 years ago
ycding
▴ 20
0
votes
2
replies
1.6k
views
Get normalized COUNTS Deseq2
deseq2
normalized counts
updated 7.2 years ago by
Steve Lianoglou
★ 13k • written 7.2 years ago by
anaQ
• 0
0
votes
1
reply
1.7k
views
Subset bam file in R
rsamtools
genomicalignments
genomicranges
updated 7.2 years ago by
Michael Lawrence
★ 11k • written 7.2 years ago by
ferbecneu
• 0
0
votes
6
replies
2.6k
views
large range of LFC in DESeq2
deseq2
lfc
betaprior
updated 3.3 years ago by
Michael Love
43k • written 7.2 years ago by
Mariaxi
• 0
2
votes
1
reply
1.5k
views
Bug in follow and precede
software error
genomicranges
iranges
updated 7.2 years ago by
Valerie Obenchain
★ 6.8k • written 7.2 years ago by
abc
• 0
0
votes
0
replies
1.5k
views
Job:
Bioinformatician ('CHBIO15) (m/f)
bioinformatician job
Linux
NGS
Job
7.2 years ago
l.brown
▴ 10
0
votes
3
replies
4.8k
views
Data normalization and transformation using DESeq2
deseq2
normalization
rnaseq
rlog transformation
variancestabilizingtransformation
7.2 years ago
chiara.facciotto
• 0
2
votes
2
replies
1.3k
views
DESeq results gives all genes
deseq2
design matrix
results
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
evocanres
• 0
0
votes
9
replies
4.3k
views
Featurecounts issue for counting exons: Not matching total counts mapped for specific gene
featurecounts
Rsubread
ggbio
updated 7.2 years ago by
Wei Shi
★ 3.6k • written 7.2 years ago by
A
▴ 60
3
votes
6
replies
2.9k
views
Controlling numerical covariates: differential gene expression with limma voom
limma
voom
differential gene expression
rnaseq
R
updated 7.2 years ago by
mikhael.manurung
▴ 280 • written 7.2 years ago by
Onyi Ukay
• 0
5
votes
2
replies
3.8k
views
non-integer counts for edgeR
edgeR
13.7 years ago • updated 7.2 years ago
Gordon Smyth
53k
7
votes
7
replies
10k
views
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2
LRT
rnaseq
design
reduced model
updated 7.2 years ago by
evocanres
• 0 • written 8.8 years ago by
I.Castanho
▴ 50
0
votes
0
replies
1.2k
views
Plotting motif enrichment vs background - Jaspar core vertebrates
pwm
motifs
jaspar
meme
motif analysis
7.2 years ago
rbronste
▴ 60
1
vote
3
replies
984
views
DeSeq2 with extremely variable samples
deseq2
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
Helene
• 0
0
votes
1
reply
1.6k
views
DESeq2 PCA plotting
deseq2
michael love
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
sam.far.7
• 0
0
votes
1
reply
1.3k
views
DESeq2 then fdrtool
deseq2
fdrtool
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
bioinfo
• 0
0
votes
3
replies
1.4k
views
collapseReplicates changes order of factors
deseq2
bug
7.2 years ago
António Miguel de Jesus Domingues
▴ 510
0
votes
3
replies
3.4k
views
How can I read in BEAST nexus tree with treeio and get all node values
treeio
beast
nexus
ips
OutbreakTools
7.2 years ago
sknu003
• 0
0
votes
2
replies
4.5k
views
[clusterprofiler] Transformation from ENSEMBL ID to entrez ID or Symbol got reduced number of genes
clusterprofiler
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
tenger929
• 0
0
votes
3
replies
1.2k
views
RNA seq analysis
rnaseq
machine learning
7.2 years ago
marak
• 0
0
votes
2
replies
1.7k
views
(GOSemSim package) secondary GO terms generating NA values
gosemsim
updated 7.2 years ago by
Guangchuang Yu
★ 1.2k • written 7.2 years ago by
l.willianpacheco
• 0
4
votes
4
replies
2.1k
views
Interpreting mroast results
mroast
limma
roast
7.2 years ago
SB
• 0
0
votes
6
replies
1.7k
views
Physical position to gene positions
bioconductor
molecular biology
snps
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
jebreen20
• 0
3
votes
4
replies
2.0k
views
Different annotation obtained from hgu133a2.db and affymetrix annotation release
annotation
hgu133plus2.db
affymetrix microarrays
micorarray
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
2323982403
▴ 60
0
votes
3
replies
1.7k
views
Installing lpsymphony on Mac OS X
R
lpsymphony
mac os x
updated 7.2 years ago by
Wolfgang Huber
★ 13k • written 7.2 years ago by
tohsumi
• 0
1
vote
3
replies
6.3k
views
DESeq2 estimateSizeFactors with control genes
deseq2
differential gene expression
controls
references
updated 10 months ago by
sofia.rigou
• 0 • written 7.2 years ago by
cris.kgs
• 0
0
votes
1
reply
1.3k
views
Chromosome arm loss and --maxhomozygousloss default
Purecn
maxhomozygousloss
7.2 years ago
twtoal
▴ 10
1
vote
2
replies
2.2k
views
Error with untar2 that blocks the installation of GO.db on Windows (R 3.5, Bioc 3.8) for using clusterProfiler
go.db
clusterprofiler
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
Leonardo Collado Torres
★ 1.1k
2
votes
4
replies
3.4k
views
Filtering, minimum sample number, and condition in edgeR
edger
filtering
updated 7.2 years ago by
Ryan C. Thompson
★ 7.9k • written 7.2 years ago by
rproendo
▴ 30
1
vote
0
replies
1.0k
views
create null sequences with gkmSVM for mouse genome mm10
gkmSVM
7.2 years ago
fusion.slope
▴ 10
5
votes
2
replies
2.2k
views
Correct usage of tximport counts in edgeR without offset matrix.
tximport
edgeR
rna-seq
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
ttekath
• 0
0
votes
3
replies
1.6k
views
How to clear a cached S4 method
devtools
S4
methods
cache
7.2 years ago
Michael Steinbaugh
▴ 90
0
votes
6
replies
2.3k
views
How to prepare .vcf for seqCAT
seqCAT
variantannotation
gatk
updated 7.2 years ago by
erikfas
▴ 30 • written 7.2 years ago by
abe
• 0
1
vote
1
reply
1.2k
views
Calling a package specific function in a for loop
drimseq
swimming downstream
for loop
sapply
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
georgewwp
• 0
1
vote
2
replies
1.5k
views
Comparing more than 2 experimental groups with MEDIPS?
medips
medip-seq
dna methylation
dmr analysis
updated 7.2 years ago by
Lukas Chavez
▴ 570 • written 7.2 years ago by
mtefit
• 0
2
votes
4
replies
2.3k
views
Inconsistent result between limma/voom and DESeq2
deseq2
limma
voom
limma-voom
rnaseq
updated 7.2 years ago by
Gordon Smyth
53k • written 7.2 years ago by
bharata1803
▴ 60
3
votes
4
replies
2.7k
views
Error: 'biocValid' is not an exported object from 'namespace:BiocManager'
biocmanager
updated 7.2 years ago by
shepherl
4.3k • written 7.2 years ago by
mariatuffy
• 0
0
votes
2
replies
1.6k
views
Rsubread installation failed
r
package installation
7.2 years ago
justinkablan225
▴ 10
46,741 results • Page
237 of 935
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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/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC
by
Ben
• 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis
by
James W. MacDonald
68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
varying.mastodon.isyn
• 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
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
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