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
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1
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1.3k
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similar limma's contrast.fit function for lme (mixed effect model) object
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updated 9.9 years ago by ▴ 50 • written 18.6 years ago by ★ 1.0k
2
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3
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Loading BSgenome.Hsapiens.UCSC.hg19 package
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updated 9.9 years ago by 25k • written 9.9 years ago by • 0
0
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3
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summarizeOverlaps on stranded paired end RNAseq data
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9.9 years ago vedran.franke • 0
1
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4
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Generate sample data based on DESeq2 result
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updated 9.9 years ago by 43k • written 9.9 years ago by ▴ 60
0
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How to use CP:REACTOME subcategory under category C2 in Broad list (globaltest)
globaltest
9.9 years ago Aditya Saxena ▴ 10
0
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3
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Error in "getZScores()" while running FourCSeq package
fourcseq
9.9 years ago MaddieS • 0
0
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2
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write.csv of GPL570 using bioconducter package and GEOquery
write.csv
updated 9.9 years ago by 68k • written 9.9 years ago by • 0
0
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14
replies
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Pbase: AddIdentificationData. How can I use MSnId objects (filtered psm) to build the Proteins database
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updated 9.9 years ago by ▴ 80 • written 9.9 years ago by • 0
1
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0
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1.4k
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performance of limma gene set analysis in relation to Tarca et al. (2013)
limma genesetenrichment
updated 9.9 years ago by ★ 13k • written 9.9 years ago by ▴ 160
1
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4
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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
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2
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3.5k
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DESeq - Change PCA axis from PasillaGuide to PC3 and PC4
deseq pca pasilla
updated 9.9 years ago by ▴ 180 • written 9.9 years ago by • 0
0
votes
2
replies
2.1k
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Gene symbol annotation not converted for intergenic SNPs with multiple genes
annotation variantannotation rstudio
updated 9.9 years ago by ★ 6.8k • written 9.9 years ago by • 0
1
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5
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Multiple condition analysis
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9.9 years ago John ▴ 30
4
votes
2
replies
4.2k
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DESeq2/SAMSeq - analysing subset of genes from RNASeq dataset
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updated 9.9 years ago by 43k • written 9.9 years ago by • 0
0
votes
1
reply
1.5k
views
Error message in makeTxDbFromGFF()
iranges genomicfeatures
updated 9.9 years ago by 43k • written 9.9 years ago by • 0
2
votes
6
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Density plots microarray
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updated 9.9 years ago by ★ 1.1k • written 9.9 years ago by ▴ 150
0
votes
3
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3.3k
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DiffBind Normalization by bFullLibrarySize
atac-seq
updated 9.9 years ago by ★ 5.2k • written 9.9 years ago by ▴ 10
2
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6
replies
3.3k
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GOexpress: GO_analyse function throws Error: Space required after the Public Identifier
goexpress
updated 9.9 years ago by ▴ 350 • written 9.9 years ago by ▴ 20
7
votes
2
replies
2.0k
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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 53k • written 9.9 years ago by ★ 7.9k
0
votes
4
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2.9k
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Segfault error when loading xcms and mzR packages
software error mzr xcms
9.9 years ago pmartin • 0
0
votes
2
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6.3k
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What does this mean?
software error
9.9 years ago xlyan011 • 0
0
votes
0
replies
2.1k
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Cannot install package "mzR"
mzR Rcpp
9.9 years ago cheng68 • 0
1
vote
2
replies
1.2k
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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 ★ 11k • written 9.9 years ago by • 0
1
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2
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Diffbind - retrieving individual sample RPKM values for differentially bound sites
diffbind
updated 9.9 years ago by ★ 5.2k • written 10.0 years ago by ▴ 10
1
vote
1
reply
2.3k
views
blocking factors in diffbind for edgeR and DESeq2 analysis
diffbind
updated 9.9 years ago by ★ 5.2k • written 10.0 years ago by • 0
1
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2
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2.0k
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error in frameCounting in riboSeqR
riboseqr ribosome profiling
updated 9.9 years ago by ▴ 180 • written 10.0 years ago by • 0
2
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4
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read bead-level data directly by lumi
bead-level GEO lumi
updated 9.9 years ago by ★ 6.6k • written 9.9 years ago by • 0
2
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3
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Adjusted p-value output from Limma different from output using p.adjust?
Limma R microarray
9.9 years ago Cale Reid ▴ 10
4
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4
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filterVcf by sample id
variantannotation
updated 9.9 years ago by ★ 6.8k • written 9.9 years ago by ▴ 470
0
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0
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1.3k
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getGEO is taking too long time for a file that is already locally cached
getgeo r
9.9 years ago alptaciroglu ▴ 50
8
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3
replies
19k
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edgeR normalization method
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updated 9.9 years ago by ★ 29k • written 9.9 years ago by ▴ 20
0
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Job: Post Doctorate Position Available
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9.9 years ago recruitment • 0
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Job: Position Available For a Bioinformatician
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9.9 years ago recruitment • 0
5
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3
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ribosome profiling and rna seq data with Deseq2 package
deseq2
updated 9.9 years ago by ▴ 610 • written 9.9 years ago by ▴ 20
0
votes
1
reply
1.6k
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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
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2
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1.9k
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readIllumina couln't read bead-level txt file from GEO raw data
beadarray bead-level GEO lumi
updated 9.9 years ago by ★ 6.6k • written 9.9 years ago by • 0
2
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2
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2.1k
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data acquisition using biomaRt
biomart
9.9 years ago maedakus ▴ 10
0
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1
reply
2.5k
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Pathview: visualization of data
pathview data visualization
updated 9.9 years ago by ★ 1.6k • written 9.9 years ago by ★ 4.1k
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4
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About "mutationsignature" package, how to use it with only one type of cancer?
mutational signature
updated 9.9 years ago by ★ 1.3k • written 9.9 years ago by • 0
0
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2
replies
2.2k
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mutational signatures problems
bsgenome readvcf tcga annotation somaticsignatures
updated 16 months ago by • 0 • written 9.9 years ago by • 0
0
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5
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Missing binaries for AnnotationData packages?
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9.9 years ago Jenny Drnevich ★ 2.0k
0
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1
reply
2.4k
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FlowWorkspace and norm2Filter
flowcytometry opencyto flowworkspace flowcore
9.9 years ago Jiang, Mike ★ 1.3k
0
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1
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PatientGeneSet installation problem
package installation
updated 9.9 years ago by ★ 8.2k • written 9.9 years ago by • 0
1
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2
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How can I see that my samples is normalized or not?
Normalization ExpressionSet Series
updated 9.9 years ago by 68k • written 9.9 years ago by • 0
2
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5
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GenVisR Installation error message
genvisR
9.9 years ago Deep Adhya ▴ 20
3
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1
reply
1.6k
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Limma -decideTests interpretation for M-values
limma decidetests methylation
updated 9.9 years ago by 21k • written 9.9 years ago by ▴ 10
0
votes
2
replies
1.6k
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DiffBind: same numbers in dba.overlap
diffbind dba.overlap
9.9 years ago Udi Landau ▴ 30
3
votes
2
replies
2.1k
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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
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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…
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Answer: When to use edgeR or limma
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