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votes
1
reply
1.2k
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Counting the number of paralogues for mouse genes gives me the wrong frequency
R
bioconductor
biomart
bioinformatics
8.0 years ago
Jack
• 0
0
votes
3
replies
1.4k
views
DESeq2 Model matrix not full rank error despite fully-crossed experimental design
deseq2
multiple factor design
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
maherr
• 0
2
votes
4
replies
2.1k
views
calling combineFeatures twice causes duplicate row.names
msnbase
duplicate
rforproteomics
updated 8.0 years ago by
Laurent Gatto
1.6k • written 8.0 years ago by
joris.vanhoutven
▴ 10
0
votes
0
replies
1.4k
views
Error using gosummaries (GOsummaries) on small log2 fold change values
gosummaries
gene ontology
enrichment analysis
8.0 years ago
jan.soderman
• 0
0
votes
9
replies
4.3k
views
Upgrade bioconductor 3.2 to 3.3
bioclIte
tximportData
updated 8.0 years ago by
hauken_heyken
▴ 80 • written 9.6 years ago by
jarod_v6@libero.it
▴ 40
1
vote
1
reply
1.6k
views
Ensembl transcripts returned by getBM not matching the biomart website
ensembl
transcripts
getbm
biomart
8.0 years ago
hihi.joshi
• 0
0
votes
3
replies
2.6k
views
Barcodeplot limma function using two logFC lists
limma
edger
barcodeplot
gene set enrichment
mroast
updated 8.0 years ago by
Gordon Smyth
53k • written 8.0 years ago by
srmaruyama
• 0
1
vote
1
reply
1.8k
views
Error: BiocParallel errors; first error: invalid 'times' value
MBASED
biocparallel
updated 8.0 years ago by
Martin Morgan
25k • written 8.0 years ago by
skhalid7
▴ 10
0
votes
0
replies
601
views
Error in cgdsr for getting clinical data
cgdsr
8.0 years ago
Yusuke Kuwahara
• 0
0
votes
2
replies
2.2k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE
ReactomePA
enrichMap
enrichPathway
updated 8.0 years ago by
Guangchuang Yu
★ 1.2k • written 8.0 years ago by
jan.soderman
• 0
0
votes
3
replies
1.1k
views
what happened in limma or Desq2 for ANOVA
limma
updated 8.0 years ago by
Gordon Smyth
53k • written 8.0 years ago by
Bioinformatics
▴ 30
0
votes
1
reply
1.0k
views
getPages() in SNPediaR returning a lexical error
software error
bioconductor
R
snpediar
getpages
8.0 years ago
johnzaharick
• 0
0
votes
0
replies
1.3k
views
batch blast matrix of protein sequences from R
R
blast
blastsequences
protein
8.0 years ago
andres.susrud
• 0
0
votes
0
replies
1.2k
views
Contrast matrix for a continuous covariate - for EGSEA algorithm
design and contrast matrix
egsea
8.0 years ago
Stefano Mangiola
▴ 40
0
votes
1
reply
904
views
calculateQCmetrics doesn't accept `numeric` `feature_controls` in scater 1.6.2
scater
updated 8.0 years ago by
Aaron Lun
★ 29k • written 8.0 years ago by
Andrew_McDavid
▴ 280
0
votes
2
replies
1.4k
views
Installing DEseq packeges under windows10 , can't find library after succesful install
deseq2
package installation
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
susannehoward
• 0
0
votes
0
replies
1.0k
views
PWMEnruch: Error in getPromoters(organism)
r
pwmenrich
8.0 years ago
prp291
• 0
0
votes
0
replies
1.0k
views
MSGFgui loading problem (cannot upload or add data)
software error
R
msgfgui
8.0 years ago
laural710
• 0
2
votes
4
replies
1.9k
views
GOexpress - Trouble with subset_scores result (<0 rows>)
GOexpress
subset_scores
<0 rows>
8.0 years ago
sina.zboron
• 0
2
votes
4
replies
6.7k
views
Age covariate continuous vs. categorical
deseq2
linear model
covariates
age
design model
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
L_K
• 0
1
vote
1
reply
967
views
rss feed for new packages
RSS
updated 8.0 years ago by
nitesh.turaga
▴ 140 • written 8.0 years ago by
Andreas Leha
▴ 30
3
votes
5
replies
3.2k
views
MasigPro and estimation of theta for negative binomial law
R
masigpro
edgr
rnaseq
negative binomial model
8.0 years ago
nicolas.hipp
▴ 10
0
votes
5
replies
2.2k
views
Error when use getSegmentReadCountsFromBAM
targeted sequencing
cn.mops
8.0 years ago
jinxinhao1988
• 0
0
votes
4
replies
2.1k
views
limma package for DEGs analysis
limma
updated 8.0 years ago by
Gordon Smyth
53k • written 8.0 years ago by
lawarde.ankita1
▴ 30
0
votes
3
replies
1.9k
views
edgeR:fitted and partial expression values
edgeR
cpm
edger
fitted model
explained variance
updated 8.0 years ago by
Gordon Smyth
53k • written 8.0 years ago by
alakatos
▴ 130
1
vote
6
replies
2.1k
views
how to analysis htseq-count
deseq2
written 8.0 years ago by
Bioinformatics
▴ 30
0
votes
3
replies
4.8k
views
Unable to reroot RAxML tree with ggtree
ggtree
raxml
reroot
tree
8.0 years ago
kevin.liam.keegan
• 0
0
votes
3
replies
2.1k
views
scalability of edgeR on RRBS methylation data
edgeR
methyation
RRBS
updated 8.0 years ago by
Gordon Smyth
53k • written 8.0 years ago by
osa.zuta
▴ 40
14
votes
9
replies
5.0k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma
rna-seq
removebatcheffect()
updated 8.0 years ago by
alakatos
▴ 130 • written 9.7 years ago by
Ekarl2
▴ 80
0
votes
4
replies
4.7k
views
where is mart hsapiens_gene_ensembl ?
bioconductor
8.0 years ago
paul28
• 0
3
votes
2
replies
1.8k
views
Subset SummarizedExperiment Objects by Metadata
summarizedexperiment
8.0 years ago
Lucas Schiffer
▴ 240
1
vote
2
replies
4.3k
views
Applying SVA to RNA-Seq dataset
DESeq2
sva
svaseq
batch effect correction
8.0 years ago
L_K
• 0
0
votes
2
replies
1.5k
views
issue retrieving metadata after psetdiff function
grangeslist
granges
8.0 years ago
andreag1987
• 0
1
vote
0
replies
1.5k
views
ClusterProfiler Annotation Problem
ClusterProfiler
8.0 years ago
papanton
▴ 10
2
votes
2
replies
2.3k
views
BiomaRT URLs down? 404 Not Found
biomart
bioconductor
support.bioconductor.org
biocinstaller
install
8.0 years ago
n.pantelireis16
• 0
0
votes
2
replies
1.5k
views
error when using M-values in ChAMP
ChAMP
updated 21 months ago by
hortense96
• 0 • written 8.0 years ago by
a.mcneill
• 0
0
votes
6
replies
2.8k
views
Combining two MSnSet
msnbase
8.3 years ago • updated 8.0 years ago
kamal.fartiyal84
▴ 10
3
votes
4
replies
10k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 23 months ago by
JG13
• 0 • written 12.5 years ago by
Makis Motakis
▴ 30
0
votes
1
reply
1.7k
views
Rsubread Read Bam and filter reads by TAG field
Rsubread
featurecounts
featurerequest
8.0 years ago
alessandro.pastore
▴ 20
2
votes
1
reply
2.8k
views
Error in DESeq2 plotMA from object subset
deseq2
maplot
subset
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
rbronste
▴ 60
0
votes
1
reply
1.2k
views
Affy ClariomD human transcriptome annotation
affy
annotation
pd.clariom.d.human
updated 8.0 years ago by
James W. MacDonald
68k • written 8.0 years ago by
anitabaery
• 0
1
vote
2
replies
2.0k
views
DESeq2 design & model matrix not full rank - am I nesting correctly?
deseq2
model matrix
experimental design
multiple factor design
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
amye107
• 0
1
vote
1
reply
1.7k
views
Including taxa names in heatmap in metagenomeseq
gut microbiome
heatmap
metagenomeseq
updated 8.0 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.0 years ago by
arguello.rguez
• 0
1
vote
2
replies
2.3k
views
Gviz: Add label/title to GenomeAxisTrack
Gviz
celegans
updated 8.0 years ago by
Robert Ivanek
▴ 750 • written 8.0 years ago by
alex.gos90
▴ 10
0
votes
1
reply
3.8k
views
DESeq2 design model/contrasts question 3 level condition
deseq2
model design
differential gene expression
experimental design
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
L_K
• 0
0
votes
0
replies
1.4k
views
I need to measure distance of PAR-CLIP data to RNA regions
parclip
bedtools
bed files
gff3
8.0 years ago
linuxborg2
• 0
0
votes
2
replies
1.3k
views
DESeq2, no significantly DE genes
deseq2
differential expression
adjusted pvalue
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
A
▴ 60
1
vote
2
replies
4.5k
views
edgeR::cpm - Doesn't work on DGEList after update
edger
updated 8.0 years ago by
Gordon Smyth
53k • written 8.0 years ago by
nilssonp386
• 0
3
votes
11
replies
5.7k
views
GEOquery http:// url error
geoquery
error
getgeo
microarray
geo
updated 8.0 years ago by
Sean Davis
21k • written 8.8 years ago by
jblack29
• 0
0
votes
1
reply
2.1k
views
GEOquery getGEO 404
geoquery
geoquery error message
updated 8.0 years ago by
Sean Davis
21k • written 8.0 years ago by
anthony.nash
▴ 20
46,717 results • Page
286 of 935
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Comment: Joining different datasets and analyzing using the group-specific condition effe
by
jason.chai
• 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts)
by
Luca
• 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Comment: Clarification on counting in Rsubread (featureCounts)
by
Gordon Smyth
53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts)
by
Frances Turner
▴ 20
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Comment: Incosistencies in buildSNNGraph() function
by
ATpoint
★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
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