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0
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20
replies
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VariantAnnotation function getTranscriptSeqs() gives error "object '.makeUCSCTxListFromGRangesList' not found"
variantannotation
8.8 years ago • updated 8.6 years ago
Tjeerd Dijkstra
• 0
52
votes
20
replies
44k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 8.0 years ago by
adam
• 0 • written 8.4 years ago by
AB
▴ 110
13
votes
20
replies
3.6k
views
cellCounts() function floating point error
Rsubread
2.0 years ago • updated 21 months ago
J-E
• 0
0
votes
20
replies
5.1k
views
ttest or fold change
updated 20.4 years ago by
Garrett Frampton
▴ 20 • written 20.4 years ago by
Jason Hipp
▴ 40
2
votes
20
replies
2.8k
views
plotPCA in DESeq2
software error
deseq2
3.9 years ago
yueli7
▴ 20
0
votes
20
replies
2.4k
views
help with reduction operation using IRanges/GRanges
12.1 years ago
Abhishek Pratap
▴ 410
11
votes
20
replies
4.2k
views
Detection p-value: difference between limma and lumi packages
p-value
detection
updated 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
Eleni Christodoulou
▴ 150
1
vote
20
replies
3.7k
views
Deseq2 installed, but there is no package called ‘Biostrings’
DESeq2
Install
updated 19 months ago by
James W. MacDonald
65k • written 19 months ago by
Hannah000111
• 0
0
votes
20
replies
2.2k
views
Different DESeq2 results (both FC and pvalue) by changing col/row orders in input
DESeq2
23 months ago
Weisheng
• 0
0
votes
20
replies
12k
views
BiocInstaller’ is not available (for R version 3.2.2)
biocinstaller
8.7 years ago
anikumar.murugan
• 0
5
votes
20
replies
3.1k
views
matching of AAStringSet vs. another AAStringSet
biostrings
AAStringset
7.5 years ago • updated 7.4 years ago
tobias.kockmann
▴ 20
0
votes
20
replies
2.4k
views
Odd contrast; does it make statistical sense?
edgeR
edgeR
updated 2.2 years ago by
Gordon Smyth
50k • written 10.3 years ago by
Ryan C. Thompson
★ 7.9k
13
votes
20
replies
14k
views
Can I feed TCGA normalized count data to EdgeR for differential gene expression analysis
EdgeR
TCGA
normalized count
updated 9.2 years ago by
alakatos
▴ 130 • written 9.2 years ago by
ycding
▴ 10
5
votes
20
replies
3.1k
views
derfinder: fullCoverage() problems
derfinder
updated 9.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.6 years ago by
jessica.hekman
▴ 40
2
votes
20
replies
5.4k
views
Important r packages not available for R version 3.1.1
exonmap
exon array analysis
bioconductor
9.2 years ago
svlachavas
▴ 830
8
votes
20
replies
5.7k
views
Issue when import genomic features from the file :Error in parseURI("") : cannot parse URI (issue resolved)
genomicfeatures
xml
libxml2
7.2 years ago
JunLVI
▴ 40
8
votes
20
replies
4.7k
views
Using DiffBind blacklists and greylists with results mapped to BDGP6
DiffBind
updated 2.3 years ago by
Rory Stark
★ 5.2k • written 3.4 years ago by
Sam
▴ 10
2
votes
20
replies
10k
views
problem loading lumi package, Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'
lumi
updated 9.0 years ago by
laseaman
• 0 • written 9.5 years ago by
lucashusquin
▴ 10
0
votes
20
replies
2.8k
views
affy won't load
GUI
affy
GUI
affy
15.9 years ago
jason smith
▴ 50
1
vote
20
replies
2.0k
views
Time-course, comparison of two groups
edgeR
14 months ago • updated 13 months ago
boczniak767
▴ 720
4
votes
20
replies
2.5k
views
scaling loess curves
HiTC
gothic
diffhic
HiC
8.7 years ago
Bogdan
▴ 670
0
votes
20
replies
6.2k
views
SummarizeOverlaps in R
summarizeoverlaps
Bam
rstudio
updated 8.8 years ago by
Jake
▴ 90 • written 8.8 years ago by
Lillyhchen
▴ 10
6
votes
19
replies
3.6k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2
timecourse
multiple factor design
RNAseq analysis
differential gene expression
updated 6.6 years ago by
Gavin Kelly
▴ 680 • written 6.6 years ago by
c.nicole
▴ 50
0
votes
19
replies
2.1k
views
flowQ loading error after installing ImageMagick
flowQ
flowQ
updated 11.2 years ago by
Dan Tenenbaum
★ 8.2k • written 11.2 years ago by
Guest User
★ 13k
3
votes
19
replies
5.7k
views
lfcShrink and factors with multiple levels
deseq2
lfcshrink
relevel
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
mat.lesche
▴ 90
14
votes
19
replies
19k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2
annotation
granges
updated 2.3 years ago by
Nadine
▴ 60 • written 9.6 years ago by
Darya Vanichkina
▴ 120
6
votes
19
replies
7.9k
views
biomaRt SNP (rs ID) -to-HGNC symbol mapping question
biomart
9.6 years ago
k.askland
▴ 20
1
vote
19
replies
25k
views
Import bamfiles for RNAsequencing analysis
R
rnaseq
bam file
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
Merlin
▴ 10
2
votes
19
replies
2.7k
views
tximport returns NA counts
tximport
6.5 years ago
leonfodoulian
• 0
3
votes
19
replies
2.3k
views
EBImage computeFeatures error
ebimage
image processing
computefeatures
updated 5.5 years ago by
Mike Smith
★ 6.5k • written 5.5 years ago by
Mathieu Gendarme
▴ 20
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 16 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
19
replies
1.8k
views
Quickest way to convert IDs in a data frame?
updated 10.8 years ago by
Thomas Girke
★ 1.7k • written 10.8 years ago by
enricoferrero
▴ 660
0
votes
19
replies
3.5k
views
Analysis and annotation (full) of Affymetrix Mouse Exon 1.0 ST arrays
Annotation
cdf
Annotation
cdf
updated 11.9 years ago by
James W. MacDonald
65k • written 11.9 years ago by
Andreas Heider
▴ 340
0
votes
19
replies
1.9k
views
expresso: performing RMA on NON-Affy data?
updated 15.1 years ago by
James W. MacDonald
65k • written 15.1 years ago by
J.delasHeras@ed.ac.uk
★ 1.9k
7
votes
19
replies
17k
views
Can't load package "org.Hs.eg.db"
org.Hs.eg.db
updated 2.8 years ago by
insanhabib1996
• 0 • written 8.7 years ago by
sjmonkley
▴ 40
14
votes
19
replies
8.9k
views
DESeq2 Model Design
DESeq2
linear model
model
updated 3.0 years ago by
Michael Love
42k • written 9.5 years ago by
andrew.j.skelton73
▴ 370
3
votes
19
replies
3.6k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma
batch effect
covariates
contrast
differential gene expression
7.1 years ago
mheydarpour
▴ 10
0
votes
19
replies
1.9k
views
Paired Difference Analysis
deseq2
R
differential gene expression
6.8 years ago • updated 6.7 years ago
nhua
• 0
5
votes
19
replies
6.0k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 9 months ago by
liz.lamarca
• 0 • written 2.8 years ago by
kwangbom
▴ 10
2
votes
19
replies
2.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome
DESeq
Microbiome
DESeq
updated 10.1 years ago by
Michael Love
42k • written 10.1 years ago by
Sophie Josephine Weiss
▴ 130
0
votes
19
replies
2.2k
views
Help with using CRISPRseeker
CRISPR
updated 4.7 years ago by
Julie Zhu
★ 4.3k • written 4.8 years ago by
sharvari gujja
▴ 40
9
votes
18
replies
2.3k
views
bam2CTSS function error from CAGEr package
cager
5.6 years ago
Pengcheng Yang
▴ 60
0
votes
18
replies
2.6k
views
DESeq2: Possible issue with colData and sorting
deseq2
summarizedexperiment
updated 7.7 years ago by
Martin Morgan
25k • written 7.7 years ago by
henrik.seidel
▴ 40
6
votes
18
replies
3.3k
views
biomaRt - getBM - biomart= ENSEMBL_MART_FUNCGEN !!! NOT WORKING!!!
bioconductor
biomart
problem with connection
updated 7.9 years ago by
Dan Staines
▴ 70 • written 7.9 years ago by
juan-pablo.cerapio-arroyo
▴ 10
7
votes
18
replies
8.4k
views
Differential expression analysis: Continuous variables
DESeq
EdgeR
limma
8.6 years ago
Radek
▴ 90
3
votes
18
replies
3.1k
views
DESeq2 filter out my expression gene
deseq2
updated 8.3 years ago by
Michael Love
42k • written 8.3 years ago by
jarod_v6@libero.it
▴ 40
0
votes
18
replies
2.4k
views
LPE error caused by gcRMA [Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length zero]
Cancer
gcrma
LPE
affylmGUI
Cancer
gcrma
LPE
affylmGUI
updated 15.5 years ago by
Charlie Whittaker
▴ 70 • written 15.5 years ago by
Wolfgang Huber
★ 13k
0
votes
18
replies
4.5k
views
cn.MOPs: Error in value[[3L]](cond) :
cn.mops
updated 5.8 years ago by
Günter Klambauer
▴ 540 • written 5.8 years ago by
laurabuggiotti
• 0
0
votes
18
replies
3.5k
views
extract introns
updated 12.5 years ago by
Martin Morgan
25k • written 12.5 years ago by
Yating Cheng
▴ 90
3
votes
18
replies
2.7k
views
Problem with hLICORN function of CoRegNet
network analysis
updated 8.7 years ago by
remy.c.nicolle
▴ 10 • written 8.7 years ago by
Aaerp
▴ 40
1,000 results • Page
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Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
Matthew Thornton
▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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