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0
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0
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1.8k
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brnn package (Bayesian regularization for feed-forward neural networks)
R machine learning brnn caret
7.6 years ago elisa.micarelli ▴ 10
6
votes
7
replies
3.7k
views
Differences between RTCGA and TCGAbiolinks data
r survival analysis rtcga tcgabiolinks mirna-seq
7.6 years ago atakanekiz ▴ 30
0
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0
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1.3k
views
Error while extracting pseudo amino acid composition using protr
r source code error
7.6 years ago shreyasarkar0 • 0
4
votes
5
replies
7.3k
views
Up/Down Regulated GeneList from edgeR and R
edger R Up reg genelist
updated 7.6 years ago by 53k • written 7.6 years ago by • 0
0
votes
0
replies
1.2k
views
Inter-run calibration in HTqPCR R package
htqpcr R
7.6 years ago dbarscortina • 0
2
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1
reply
2.8k
views
Error in TCGAquery of TCGAbiolinks Package
software error bioconductor tcgabiolinks tcga r
updated 7.7 years ago by ▴ 90 • written 7.7 years ago by ▴ 60
2
votes
3
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1.1k
views
How can I check the quality of code I have written? How to QC?
R limma bioconductor
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 10
0
votes
5
replies
2.1k
views
CSAW Spike In Normalization: Error in .local(object, ...) : library sizes of 'se.out' and 'object' are not identical
csaw software error R chip-seq bioconductor
updated 7.7 years ago by ★ 29k • written 7.7 years ago by • 0
3
votes
6
replies
1.5k
views
help DESeq2 model design
deseq2 R
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 20
2
votes
3
replies
3.5k
views
Bioconductor local installation, R versions
R bioconductor local local installation centos7
updated 7.7 years ago by 68k • written 7.7 years ago by ▴ 10
1
vote
7
replies
1.7k
views
Unable to move temporary installation R issue
software error R
updated 7.7 years ago by 25k • written 7.7 years ago by • 0
1
vote
2
replies
1.5k
views
Request to remove requirement for gr to have widths 1 in BSseq constructor
bsseq r package
updated 7.7 years ago by • 0 • written 7.7 years ago by ▴ 140
0
votes
5
replies
1.8k
views
How to simulate time course RNA seq data using DESeq?
deseq2 R makeexampledeseqdataset deseq
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
votes
4
replies
2.2k
views
HOW to define the "parLabVc" indices in ropls package.
R ropls
updated 7.7 years ago by ▴ 40 • written 7.7 years ago by • 0
1
vote
19
replies
30k
views
Import bamfiles for RNAsequencing analysis
R rnaseq bam file
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 10
5
votes
12
replies
10k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 120
3
votes
6
replies
6.0k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 7.7 years ago by 68k • written 7.7 years ago by ▴ 120
0
votes
5
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1.7k
views
DEseq2 differentially expressed genes have lower expression values than non-differentially expressed genes
deseq2 R
7.7 years ago lychen83 • 0
2
votes
2
replies
1.7k
views
Queries around makeOrgPackageFromNCBI
R software error annotationforge
updated 7.7 years ago by ★ 4.1k • written 7.7 years ago by • 0
2
votes
4
replies
2.6k
views
How to get sequence homology percent from a multiple sequence alignment in DECIPHER?
decipher r protein alignment
7.7 years ago reubenmcgregor88 • 0
1
vote
1
reply
4.5k
views
Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R sequencing alignment rsamtools mapping
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 10
0
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0
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1.1k
views
msa output formats for use down stream to create phylogenetic trees
R bioconductor phylogenetic
7.8 years ago cav3gh • 0
0
votes
0
replies
1.5k
views
R function to deconvolve ESI MS spectra of multiple charge large biopolymers
mass spectrometry R mzR
7.8 years ago andreas.breidbach • 0
3
votes
5
replies
2.3k
views
EdgeR: Prior degrees of freedom effect on tag wise dispersion
R edgeR rnaseq rna-seq
updated 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Setting up PLAYRDesign gives error on makeTxDbFromUCSC, error in tableNames
genomicfeatures R
7.8 years ago songshan.guo • 0
4
votes
8
replies
2.3k
views
edgeR error when trying to filter peaks with low read counts
edger R filtering
7.8 years ago camerond • 0
0
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1
reply
851
views
Please help to address the BiocCheck NOTEs
R
updated 7.8 years ago by 25k • written 7.8 years ago by ▴ 10
0
votes
4
replies
4.5k
views
featureCounts taking 4-10 hours per BAM file?
featurecounts r rnaseq
7.8 years ago octopuslegs11 • 0
0
votes
1
reply
1.5k
views
counting reads with muliple hits with SummarizeOverlaps
R seq ngs summarizeoverlaps
updated 7.8 years ago by ★ 6.8k • written 7.8 years ago by • 0
1
vote
3
replies
1.9k
views
Error biocLite() newest version of ChAMP
R bioclite champ
7.8 years ago rosa_hegi ▴ 10
0
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1
reply
1.3k
views
Detect Sites with Minimum Gap in GRanges Object
R genomicranges granges grange
7.8 years ago g.k • 0
0
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1
reply
1.3k
views
Update package permission Everytime
software error R bioconductor rmysql
7.8 years ago vivekr • 0
3
votes
2
replies
2.5k
views
Error while getFirehoseData of RTCGAToolbox package
firehose R RTCGAToolbox getFirehoseData
updated 7.8 years ago by 700 • written 7.8 years ago by ▴ 30
0
votes
1
reply
2.0k
views
Error while Installing DESeq2
software error R deseq2 rnaseq
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
votes
1
reply
607
views
Mapping genomic coordinates to protein-relative coordinates
R bioconductor
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
0
votes
0
replies
1.3k
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
7.8 years ago fawazfebin ▴ 60
2
votes
18
replies
4.4k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
7.8 years ago stephan.emmrich ▴ 10
0
votes
2
replies
3.9k
views
Can't Use "getGEO" Command Function in R Program
microarray software error bioconductor affy R
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
1
vote
2
replies
2.4k
views
Detecting Overlaps within Grange Object
r grange granges iranges
updated 7.8 years ago by ★ 11k • written 7.8 years ago by • 0
0
votes
3
replies
4.8k
views
Error when constructing DESeqDataSetFromMatrix (Error in round(assay(se)): non-numeric argument to mathematical function)
deseq2 R error
updated 7.8 years ago by 43k • written 7.9 years ago by • 0
0
votes
5
replies
27k
views
package DESeq2 installation with R.
deseq2 R package installation
updated 4.6 years ago by 43k • written 7.9 years ago by • 0
0
votes
0
replies
1.4k
views
Error in building expression set for ArrayExpress
microarray expressionset arrayexpress bioconductor r
7.9 years ago rf • 0
0
votes
2
replies
2.0k
views
unable to install "variant"
R libxml2
updated 7.9 years ago by ▴ 160 • written 7.9 years ago by • 0
2
votes
2
replies
1.9k
views
Get canonical exon locations for gene
genomicfeatures r bioconductor
updated 7.9 years ago by 68k • written 7.9 years ago by • 0
1
vote
2
replies
1.4k
views
Inserting "Biotype" into scater SCE objects
scater sce biotype R
updated 7.9 years ago by ★ 29k • written 7.9 years ago by • 0
0
votes
3
replies
2.4k
views
choose between normalization techniques for OTU counts
deseq2 normalization R edger
7.9 years ago apfelbapfel ▴ 30
0
votes
6
replies
2.3k
views
DESeq2 It is correct to use interaction term for patient variability?
deseq2 design interaction term R
written 7.9 years ago by • 0
3
votes
1
reply
864
views
Gene expression analysis
cancer R
updated 7.9 years ago by 68k • written 7.9 years ago by • 0
4
votes
0
replies
1.3k
views
News: Bioconductor at useR! 2018
conference r bioconductor News
7.9 years ago Matthew Ritchie ▴ 1000
0
votes
1
reply
1.7k
views
topGO error : could not find function "annotationFun"
topGO R
7.9 years ago User • 0
1,163 results • Page 12 of 24
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…
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/
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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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