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Views
Votes
0
votes
0
replies
1.2k
views
Visualize FlowSet by Date
FlowSet
data visualization
cellcounts
8.6 years ago
Maria
• 0
0
votes
0
replies
1.1k
views
TSCANorder return less cell number than the raw cell number
TSCAN
software error
8.6 years ago
yancychy
• 0
1
vote
1
reply
1.8k
views
Add flowclust gate to gatingset
opencyto
flowclust
updated 8.6 years ago by
Jiang, Mike
★ 1.3k • written 8.6 years ago by
pavitrarc
▴ 20
0
votes
1
reply
1.8k
views
GSEA threshold question
GSEa
r
clusterprofiler
reactomepa
8.6 years ago
bhgyu
▴ 30
0
votes
1
reply
1.3k
views
IDMapper issue in PSICQUIC
PSICQUIC
updated 8.6 years ago by
daniel.vantwisk
▴ 50 • written 8.6 years ago by
josemilezana
• 0
4
votes
9
replies
3.1k
views
Limma is doing the right way to calculate the fold change?
limma
proteomics
updated 8.6 years ago by
Laurent Gatto
1.6k • written 8.6 years ago by
Bioinformatics
▴ 30
0
votes
4
replies
3.0k
views
Gviz : sort reads in AlignmentsTracks and display reads containing indels
gviz
updated 8.6 years ago by
florian.hahne@novartis.com
★ 1.6k • written 8.7 years ago by
Aurélie GABRIEL
• 0
1
vote
3
replies
1.5k
views
find fold change in DESeq2 results
deseq2
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
ribioinfo
▴ 100
2
votes
3
replies
3.3k
views
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq
deseq2
tximport
salmon
normalization
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
kofoed
• 0
0
votes
2
replies
1.8k
views
WGCNA: error message in blockwiseModule(): address 0x0, cause 'memory not mapped'
wgcna
updated 8.6 years ago by
Peter Langfelder
★ 3.0k • written 8.6 years ago by
Razumall
• 0
0
votes
1
reply
1.4k
views
trackviewer lolliplot pie.stack
lolliplot
trackviewer
updated 8.6 years ago by
Ou, Jianhong
★ 1.3k • written 8.6 years ago by
manuel.x.duval
• 0
0
votes
0
replies
1.1k
views
Meta-Analysis chip-seq data
chip-seq
meta-analysis
8.6 years ago
rezapanahi222
• 0
0
votes
1
reply
1.6k
views
DiffBind error Error in pv.getPlotData
DiffBind
updated 8.6 years ago by
Rory Stark
★ 5.2k • written 8.6 years ago by
niu.shengyong
▴ 10
5
votes
1
reply
1.9k
views
IHWpaper: choice of `nbins=4` in `proteomics_example_analysis.R`
ihw
updated 8.6 years ago by
Nikos Ignatiadis
▴ 180 • written 8.6 years ago by
paul.johnston
▴ 10
2
votes
1
reply
2.9k
views
Correcting for Batch Effects Prior to Differential Gene Expression Analysis with limma
limma
batch effect
rna-seq
updated 8.6 years ago by
Aaron Lun
★ 29k • written 8.6 years ago by
adscheid3
• 0
2
votes
5
replies
4.4k
views
Trouble with DESeq2, edgeR, and limma not accepting zeros in input
limma
deseq2
edgeR
updated 8.6 years ago by
Gordon Smyth
53k • written 8.6 years ago by
Kaustav
• 0
0
votes
1
reply
1.0k
views
Biomart error on association gene symbols name
biomart
deseq2
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
jarod_v6@libero.it
▴ 40
0
votes
1
reply
912
views
BiocLite installation problem
bioconductor
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
Morris
▴ 10
1
vote
2
replies
1.7k
views
RStudio in Bioconductor 3.5 AMI incompatible with R 3.4
AMI
rstudio server
updated 8.6 years ago by
shepherl
4.3k • written 8.6 years ago by
Thomas Sandmann
▴ 90
0
votes
1
reply
789
views
efetch result not in character format
R
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
ezrabekele17
• 0
4
votes
6
replies
3.3k
views
Bioconductor open source policy
licenses
rankprod
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
zeehio
• 0
0
votes
4
replies
1.2k
views
Dendogram from read count to show correlation between biological replicate and samples
bioconductor
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
Jitendra
▴ 10
7
votes
12
replies
10k
views
Confused in the usage of formula in DESeq or DESeq2
deseq2
deseq
updated 8.6 years ago by
bio2001
▴ 60 • written 11.2 years ago by
skyoflcz
▴ 20
1
vote
0
replies
1.5k
views
News:
complete set of OrgDb packages have been added to AnnotationHub
bioconductor
annotationhub
orgdb
News
8.6 years ago
shepherl
4.3k
0
votes
1
reply
1.6k
views
Problem with DEGseq/samWrapper
degseq
updated 8.6 years ago by
ab.tsubaki
• 0 • written 11.1 years ago by
jovel_juan
▴ 30
5
votes
5
replies
2.1k
views
BiocParallel: messages shown only when processes finished
biocparallel
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
Johannes Rainer
★ 2.1k
0
votes
0
replies
1.5k
views
Minfi reading command error
minfi
error
command
read.metharray.exp
cdf
8.6 years ago
niutster
• 0
1
vote
9
replies
1.9k
views
DESeq2 differential gene expression with multiple development stage and tissues
deseq2
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
Jitendra
▴ 10
3
votes
4
replies
1.5k
views
deseq2 and dexseq for multiple tissue from wildtype only
deseq2
dexseq
rnaseq
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
badribio
• 0
0
votes
3
replies
3.1k
views
Inverse logFC on DESeq2 Rstudio
DESeq2
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
Luiz
• 0
0
votes
2
replies
1.3k
views
LIMMA 2x2 with time
limma
limma design matrix
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
Ahdee
▴ 60
0
votes
3
replies
3.5k
views
read count summed over exons is greater tham the gene-level read count using featureCounts
rsubread
featurecounts
exon
mRNAseq
updated 8.6 years ago by
Wei Shi
★ 3.6k • written 8.6 years ago by
inah
▴ 10
2
votes
2
replies
2.5k
views
tximport error: TXNAME from Txdb.mm10 and kallisto target_id mismatch
tximport
kallisto
txdb.mmusculus.ucsc.mm10.knowngene
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
Kaustav
• 0
2
votes
9
replies
3.3k
views
ensembldb salmon deseq2 txt2import right tool?
ensembldb
deseq2
8.6 years ago
aaron.dickey
• 0
1
vote
1
reply
5.7k
views
unable to update packages: foreign, Matrix
limma
design and contrast matrix
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
Bioinformatics
▴ 30
2
votes
3
replies
1.7k
views
PureCN can classify indel variants as germline vs. somatic ?
PureCN
indel
somatic
germline
updated 8.6 years ago by
markus.riester
▴ 130 • written 8.6 years ago by
pathkim
• 0
0
votes
0
replies
1.3k
views
Optimizing the deepSplit parameter in dynamicTreeCut
dynamicTreeCut
8.6 years ago
johnmcma
▴ 10
6
votes
16
replies
7.2k
views
DiffBind Batch Effect
diffbind
atac
8.7 years ago • updated 8.6 years ago
niu.shengyong
▴ 10
0
votes
2
replies
1.2k
views
DNAString - Long String
DNAString
updated 8.6 years ago by
Hervé Pagès
16k • written 8.6 years ago by
pgreenbank
• 0
0
votes
1
reply
826
views
Issues with .extractEnsemblReleaseFromDbVersion() and get_organism_from_Ensembl_Mart_dataset()
genomicfeatures
updated 8.6 years ago by
Hervé Pagès
16k • written 8.6 years ago by
matt.chambers42
▴ 10
0
votes
4
replies
2.0k
views
problem in installing flowclust
rstudio
flowclust
updated 8.6 years ago by
shepherl
4.3k • written 8.6 years ago by
shadhiksk
• 0
0
votes
3
replies
2.2k
views
Question about the ChIPpeakAnno:
ChIPchip
Annotation
AnnotationData
ChIPchip
Annotation
AnnotationData
updated 8.6 years ago by
jinj
• 0 • written 11.8 years ago by
Julie Zhu
★ 4.3k
3
votes
14
replies
5.0k
views
biomaRt - Error in getBM: The query to the BioMart webservice returned an invalid result
biomart
error
ensembl
bioconductor
ensembl mart
8.6 years ago
daniel.carbajo
• 0
3
votes
2
replies
1.5k
views
GenomicRanges::gaps() not working as expected
genomicranges
8.6 years ago
jfiksel
▴ 30
2
votes
3
replies
3.5k
views
BiocParallel::bplapply() performance with MulticoreParam() is worse than mclapply()
biocparallel
parallel
8.6 years ago
davide risso
▴ 980
0
votes
3
replies
1.9k
views
Error in Error in checkFullRank(modelMatrix) Deseq2
deseq2
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
michael.steffen
▴ 20
2
votes
11
replies
2.7k
views
DESeq2 polysome profiling analysis with 2 interaction terms
deseq2
sequencing
polysome profiling
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
erica
▴ 10
0
votes
2
replies
1.9k
views
Normalization for comparative transcriptomics between species
deseq2
wgcna
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
jcfnielsen
• 0
0
votes
4
replies
2.2k
views
setting contrast in edgeR for time series data
rnaseq
edger
makecontrasts
updated 8.6 years ago by
Aaron Lun
★ 29k • written 8.6 years ago by
wangzhang1988
• 0
4
votes
2
replies
1.9k
views
sc3_plot_expression, colour labels
sc3
single-cell
updated 8.6 years ago by
Vladimir Kiselev
▴ 150 • written 8.6 years ago by
cfustero
▴ 20
46,729 results • Page
328 of 935
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Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
You may want to look at the coefficients you are trying to estimate with ExploreModelMatrix: https://www.bioconductor.org/packages/relea…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
emily.wolfrum
• 0
Hi Gordon, Thanks for the quick reply. The technical or process blank samples I'm referring to are part of a set of quality control sampl…
Answer: Are individual-mouse-based statistics possible in CellChat?
by
ATpoint
★ 5.0k
Not a Bioconductor package, I commented on the crosspost at https://www.biostars.org/p/9617271/
Answer: DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
by
ATpoint
★ 5.0k
apeglm is more cumbersome than ashr as with apeglm the coefficients need to be explicitely available in the resultsNames.So, you need to re…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Martin Morgan
25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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