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7
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0
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4.6k
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Tutorial:
New edX "Data analysis for Life Sciences" module: High performance computing for reproducible genomics
annotation
genomicranges
visualization
docker
shiny
Tutorial
9.9 years ago
Vincent J. Carey, Jr.
6.7k
1
vote
1
reply
1.3k
views
similar limma's contrast.fit function for lme (mixed effect model) object
limma
limma
updated 9.9 years ago by
Gregory Warnes
▴ 50 • written 18.6 years ago by
shirley zhang
★ 1.0k
2
votes
3
replies
2.9k
views
Loading BSgenome.Hsapiens.UCSC.hg19 package
ucsc
bsgenome.hsapiens.ucsc.hg19
updated 9.9 years ago by
Martin Morgan
25k • written 9.9 years ago by
Sushant Pawar
• 0
0
votes
3
replies
2.1k
views
summarizeOverlaps on stranded paired end RNAseq data
summarizeoverlaps
9.9 years ago
vedran.franke
• 0
1
vote
4
replies
1.8k
views
Generate sample data based on DESeq2 result
deseq2
updated 9.9 years ago by
Michael Love
43k • written 9.9 years ago by
bharata1803
▴ 60
0
votes
0
replies
1.4k
views
How to use CP:REACTOME subcategory under category C2 in Broad list (globaltest)
globaltest
9.9 years ago
Aditya Saxena
▴ 10
0
votes
3
replies
1.9k
views
Error in "getZScores()" while running FourCSeq package
fourcseq
9.9 years ago
MaddieS
• 0
0
votes
2
replies
1.8k
views
write.csv of GPL570 using bioconducter package and GEOquery
write.csv
updated 9.9 years ago by
James W. MacDonald
68k • written 9.9 years ago by
yossi3758
• 0
0
votes
14
replies
3.6k
views
Pbase: AddIdentificationData. How can I use MSnId objects (filtered psm) to build the Proteins database
pbase
MsnId
mzid
msnbase
updated 9.9 years ago by
Sebastian Gibb
▴ 80 • written 9.9 years ago by
viswanathan.raghuram
• 0
1
vote
0
replies
1.4k
views
performance of limma gene set analysis in relation to Tarca et al. (2013)
limma
genesetenrichment
updated 9.9 years ago by
Steve Lianoglou
★ 13k • written 9.9 years ago by
Aditya
▴ 160
1
vote
4
replies
1.8k
views
BiocParallel 1.4.3: Error following example 4.2.1 - "Error in 0.4 * nx/tasks : non-numeric argument to binary operator"
biocparallel
9.9 years ago
lee.tibbert
▴ 20
1
vote
2
replies
3.5k
views
DESeq - Change PCA axis from PasillaGuide to PC3 and PC4
deseq
pca
pasilla
updated 9.9 years ago by
Federico Marini
▴ 180 • written 9.9 years ago by
chqr
• 0
0
votes
2
replies
2.1k
views
Gene symbol annotation not converted for intergenic SNPs with multiple genes
annotation
variantannotation
rstudio
updated 9.9 years ago by
Valerie Obenchain
★ 6.8k • written 9.9 years ago by
noor.suaini
• 0
1
vote
5
replies
1.7k
views
Multiple condition analysis
deseq2
9.9 years ago
John
▴ 30
4
votes
2
replies
4.2k
views
DESeq2/SAMSeq - analysing subset of genes from RNASeq dataset
deseq2
SAMseq
differential expression
updated 9.9 years ago by
Michael Love
43k • written 9.9 years ago by
aylj
• 0
0
votes
1
reply
1.5k
views
Error message in makeTxDbFromGFF()
iranges
genomicfeatures
updated 9.9 years ago by
Michael Love
43k • written 9.9 years ago by
jjmm1101
• 0
2
votes
6
replies
3.3k
views
Density plots microarray
microarray
limma
normalization
densityplot
updated 9.9 years ago by
Axel Klenk
★ 1.1k • written 9.9 years ago by
Eleni Christodoulou
▴ 150
0
votes
3
replies
3.3k
views
DiffBind Normalization by bFullLibrarySize
atac-seq
updated 9.9 years ago by
Rory Stark
★ 5.2k • written 9.9 years ago by
simonjean434
▴ 10
2
votes
6
replies
3.3k
views
GOexpress: GO_analyse function throws Error: Space required after the Public Identifier
goexpress
updated 9.9 years ago by
kevin.rue
▴ 350 • written 9.9 years ago by
martin.hoelzer
▴ 20
7
votes
2
replies
2.0k
views
How to evaluate a p-value histogram from treat or other threshold tests?
edger
limma
deseq2
p-value distribution
updated 9.9 years ago by
Gordon Smyth
53k • written 9.9 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
4
replies
2.9k
views
Segfault error when loading xcms and mzR packages
software error
mzr
xcms
9.9 years ago
pmartin
• 0
0
votes
2
replies
6.3k
views
What does this mean?
software error
9.9 years ago
xlyan011
• 0
0
votes
0
replies
2.1k
views
Cannot install package "mzR"
mzR
Rcpp
9.9 years ago
cheng68
• 0
1
vote
2
replies
1.2k
views
Missing data in replication
deseq2
9.9 years ago
John
▴ 30
0
votes
1
reply
1.3k
views
Integer Overflow with IRanges
iranges
r
updated 9.9 years ago by
Michael Lawrence
★ 11k • written 9.9 years ago by
remi.b.md
• 0
1
vote
2
replies
2.9k
views
Diffbind - retrieving individual sample RPKM values for differentially bound sites
diffbind
updated 9.9 years ago by
Rory Stark
★ 5.2k • written 10.0 years ago by
JD
▴ 10
1
vote
1
reply
2.3k
views
blocking factors in diffbind for edgeR and DESeq2 analysis
diffbind
updated 9.9 years ago by
Rory Stark
★ 5.2k • written 10.0 years ago by
armandorp
• 0
1
vote
2
replies
2.0k
views
error in frameCounting in riboSeqR
riboseqr
ribosome profiling
updated 9.9 years ago by
Thomas J Hardcastle
▴ 180 • written 10.0 years ago by
alper.celik
• 0
2
votes
4
replies
2.2k
views
read bead-level data directly by lumi
bead-level
GEO
lumi
updated 9.9 years ago by
Mike Smith
★ 6.6k • written 9.9 years ago by
gnilihzeux
• 0
2
votes
3
replies
3.5k
views
Adjusted p-value output from Limma different from output using p.adjust?
Limma
R
microarray
9.9 years ago
Cale Reid
▴ 10
4
votes
4
replies
2.4k
views
filterVcf by sample id
variantannotation
updated 9.9 years ago by
Valerie Obenchain
★ 6.8k • written 9.9 years ago by
Paul Shannon
▴ 470
0
votes
0
replies
1.3k
views
getGEO is taking too long time for a file that is already locally cached
getgeo
r
9.9 years ago
alptaciroglu
▴ 50
8
votes
3
replies
19k
views
edgeR normalization method
edgeR
differential expression
normalization
updated 9.9 years ago by
Aaron Lun
★ 29k • written 9.9 years ago by
Sara
▴ 20
0
votes
1
reply
1.8k
views
Job:
Post Doctorate Position Available
post doctorate
Scientist
Job
9.9 years ago
recruitment
• 0
0
votes
0
replies
1.6k
views
Job:
Position Available For a Bioinformatician
bioinformatician
jobs
Job
9.9 years ago
recruitment
• 0
5
votes
3
replies
3.2k
views
ribosome profiling and rna seq data with Deseq2 package
deseq2
updated 9.9 years ago by
Bernd Klaus
▴ 610 • written 9.9 years ago by
ecekartal89
▴ 20
0
votes
1
reply
1.6k
views
How to Plot Coverage density in one graph and to interpret normalised graphs for RNA-seq data using TEQC
normalization
9.9 years ago
arunabioinfo
• 0
1
vote
2
replies
1.9k
views
readIllumina couln't read bead-level txt file from GEO raw data
beadarray
bead-level
GEO
lumi
updated 9.9 years ago by
Mike Smith
★ 6.6k • written 9.9 years ago by
gnilihzeux
• 0
2
votes
2
replies
2.1k
views
data acquisition using biomaRt
biomart
9.9 years ago
maedakus
▴ 10
0
votes
1
reply
2.5k
views
Pathview: visualization of data
pathview
data visualization
updated 9.9 years ago by
Luo Weijun
★ 1.6k • written 9.9 years ago by
Guido Hooiveld
★ 4.1k
0
votes
4
replies
2.1k
views
About "mutationsignature" package, how to use it with only one type of cancer?
mutational signature
updated 9.9 years ago by
Julian Gehring
★ 1.3k • written 9.9 years ago by
shengfeng
• 0
0
votes
2
replies
2.2k
views
mutational signatures problems
bsgenome
readvcf
tcga
annotation
somaticsignatures
updated 16 months ago by
Danyiel
• 0 • written 9.9 years ago by
jolligoodfellow
• 0
0
votes
5
replies
1.4k
views
Missing binaries for AnnotationData packages?
binary
9.9 years ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
2.4k
views
FlowWorkspace and norm2Filter
flowcytometry
opencyto
flowworkspace
flowcore
9.9 years ago
Jiang, Mike
★ 1.3k
0
votes
1
reply
1.0k
views
PatientGeneSet installation problem
package installation
updated 9.9 years ago by
Dan Tenenbaum
★ 8.2k • written 9.9 years ago by
alessandrotestori7
• 0
1
vote
2
replies
2.0k
views
How can I see that my samples is normalized or not?
Normalization
ExpressionSet
Series
updated 9.9 years ago by
James W. MacDonald
68k • written 9.9 years ago by
vahideh
• 0
2
votes
5
replies
3.5k
views
GenVisR Installation error message
genvisR
9.9 years ago
Deep Adhya
▴ 20
3
votes
1
reply
1.6k
views
Limma -decideTests interpretation for M-values
limma
decidetests
methylation
updated 9.9 years ago by
Sean Davis
21k • written 9.9 years ago by
kraiczy
▴ 10
0
votes
2
replies
1.6k
views
DiffBind: same numbers in dba.overlap
diffbind
dba.overlap
9.9 years ago
Udi Landau
▴ 30
3
votes
2
replies
2.1k
views
Cannot use color/ fill arguments outside of aes() in ggbio karyogram layout
ggbio
9.9 years ago
Mario Saare
▴ 20
46,730 results • Page
407 of 935
Recent ...
Replies
Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Hugo Gruson
• 0
Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…
Comment: Are individual-mouse-based statistics possible in CellChat?
by
LillianaVolkman99
• 0
thank you very much. https://www.biostars.org/p/9617271/
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
My apologies, I forgot that `design.group` is not included in the final matrix, because the baseline group effects are already captured by …
Answer: Bile acid analysis with limpa
by
Gordon Smyth
53k
I am not familiar with targeted HPLC-MS and I don't know what you mean by "peak areas". If it produces standard format mass spec data from …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
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
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