Showing : R • reset
2
votes
4
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2.0k
views
Impose minimum restrictions on correlations in SingleR
single cell R SingleR
updated 5.9 years ago by ★ 29k • written 5.9 years ago by ▴ 120
5
votes
1
reply
4.4k
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 5.9 years ago by ▴ 110 • written 5.9 years ago by ▴ 20
0
votes
2
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1.3k
views
keggLink Error: linking "genes" and "reaction"
software error keggLink R
updated 6.0 years ago by 4.2k • written 6.0 years ago by • 0
0
votes
1
reply
1.5k
views
boxplot Error in Bioconductor
boxplot bioconductor R error
6.0 years ago l154359 • 0
1
vote
1
reply
1.2k
views
model matrix in limma
limma R
updated 6.0 years ago by 53k • written 6.0 years ago by ▴ 40
1
vote
1
reply
14k
views
Install Bioconductor in R studio
R
updated 6.0 years ago by ★ 4.0k • written 6.0 years ago by • 0
0
votes
1
reply
1.2k
views
CNV plot using cn.mops
cnv R plot visualization cn.mops software error
6.0 years ago ari • 0
0
votes
0
replies
1.7k
views
Job: Postdoc and PhD student in Bioinformatics/Biostatistics
NGS R statistics genomics big data Job
6.9 years ago • updated 6.0 years ago Luo Weijun ★ 1.6k
5
votes
2
replies
3.5k
views
How to perform DEseq2 on datasets without replicates or merged replicates
deseq2 R bioconductor RNA_Seq replicates
updated 6.0 years ago by ★ 1.4k • written 6.1 years ago by ▴ 30
4
votes
4
replies
2.9k
views
How I interpret this plot from pathview
pathview kegg r pathway
6.1 years ago AZ ▴ 30
1
vote
10
replies
11k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 4 months ago by 43k • written 6.1 years ago by • 0
0
votes
2
replies
2.5k
views
How to adjust and align timepoints on x-axis in the ggplot2
ggplot2 line plot x-axis data frame R
6.1 years ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
1.2k
views
News: course - Protemics with R and Bioconductor - 17-19 February 2020 in Berlin
Bioconductor R Proteomics News
6.1 years ago info ▴ 10
0
votes
5
replies
2.5k
views
readTranscriptFeatures from genomation
R Rstudio Error readTranscriptFeatures genomation
updated 6.1 years ago by ▴ 20 • written 6.1 years ago by • 0
1
vote
1
reply
2.5k
views
uploading xml file in flowworkspace
flowworkspace xml R flowjo
updated 6.1 years ago by • 0 • written 8.7 years ago by ▴ 10
3
votes
6
replies
6.5k
views
WGCNA gene significance and module membership
WGCNA R
updated 3.1 years ago by ★ 3.0k • written 6.1 years ago by • 0
0
votes
5
replies
2.7k
views
Not latest package version through 'BiocManager::install()'
debug BiocManager R pacakge R mass spectrometry
6.1 years ago wang.lingjue • 0
2
votes
0
replies
1.2k
views
SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
6.1 years ago rmash ▴ 20
0
votes
1
reply
1.2k
views
plotEigengeneNetworks WGCNA add ME labels to left side of figure
R WGCNA
6.1 years ago normingt • 0
0
votes
3
replies
1.5k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
1
vote
3
replies
1.6k
views
How can I run a paired RankProd analysis in R?
RankProd paired RNAseq R
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
4
votes
5
replies
1.4k
views
Defining the design for a complicated multi-level experiment in Limma
limma RNASeq R voom
updated 6.2 years ago by 68k • written 6.2 years ago by ▴ 60
2
votes
1
reply
11k
views
Error: status was 'SSL connect error'
bioconductor proxy macOS R RStudio
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 20
1
vote
1
reply
1.6k
views
Gviz UCSC tracks not visible
Gviz R UCSC Tracks genome locusplot
updated 6.2 years ago by ▴ 750 • written 6.2 years ago by • 0
0
votes
3
replies
2.2k
views
Writing a loop through multiple fasta files and named files (is it possible with MSGFplus?)
MSGF+ Proteomics r
updated 6.2 years ago by 25k • written 6.2 years ago by • 0
0
votes
0
replies
1.0k
views
Unable to obtain the line chart with error envelop in ggplot2 and geom_ribbon()
ggplot2 line chart R geom_ribbon()
6.2 years ago mohammedtoufiq91 ▴ 10
5
votes
8
replies
2.7k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 6.2 years ago by ★ 13k • written 6.2 years ago by ▴ 30
0
votes
0
replies
1.1k
views
Job: Bioinformatician @ University of Cambridge
cancer bioinformatics R Job
6.2 years ago Shamith.Samarajiwa ▴ 180
0
votes
3
replies
739
views
DESeq2 Identical P values in both standard and multi factor design
deseq2 r
6.2 years ago dtlloyd • 0
2
votes
2
replies
4.6k
views
How adjusted p-values are calculated in limma
limma r transcriptomics FDR statistics
updated 6.2 years ago by 53k • written 6.2 years ago by ▴ 10
2
votes
2
replies
691
views
Order of design matrix for edgeR analysis
edger r
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
0
votes
0
replies
1.3k
views
Output GenVisR mutation frequency data by gene name instead of by sample name
GenVisR mutation frequency R cancer bioconductor
6.2 years ago sheneicechang • 0
1
vote
1
reply
1.3k
views
Querying CTD database to find diseases associated with the given pathways.
CTD Database disease pathway association R programming
6.2 years ago omarrafiqued ▴ 50
2
votes
1
reply
760
views
ImportFrom statement in package
R
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
2
votes
6
replies
1.8k
views
Can't install GOSEQ (dependency problem) on CentOS 7!
goseq r package r
updated 6.3 years ago by ★ 6.6k • written 6.3 years ago by ▴ 60
3
votes
7
replies
4.5k
views
Handle missing values in the z-score matrix while plotting heatmap in the ComplexHeatmap
matrix heatmap ComplexHeatmap missing values R
updated 6.3 years ago by ▴ 290 • written 6.3 years ago by ▴ 10
0
votes
0
replies
948
views
News: Protemics with R and Bioconductor course in Berlin
R Proteomics News
6.3 years ago info ▴ 10
4
votes
3
replies
5.2k
views
Differential gene expression anlaysis?
rnaseq R normalization
updated 6.3 years ago by 53k • written 6.3 years ago by ▴ 30
0
votes
5
replies
1.8k
views
Does anyone have experience using the massiR package?
massiR microarray R probe
6.3 years ago Steve Lowe ▴ 30
0
votes
2
replies
994
views
Combining different arrays in analysis
array R normalization
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 30
4
votes
9
replies
2.4k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
1
vote
4
replies
2.5k
views
Merging two files based on the identifier column (gene symbols)?
merge files R packages gene annotations
6.3 years ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
1.2k
views
News: R/Bioconductor for Mass Spectrometry and Proteomics course in Berlin
Bioconductor R News
6.3 years ago info ▴ 10
0
votes
1
reply
1.5k
views
Installation problem in IlluminaHumanMethylation450kanno.ilmn12.hg19
IlluminaHumanMethylation450kanno.ilmn12.hg19 R
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
1
vote
1
reply
1.2k
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 30
1
vote
6
replies
3.0k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
6.3 years ago sabrina.mcnew • 0
0
votes
1
reply
1.9k
views
DiffBind dba error
DiffBind dba R error
updated 6.3 years ago by ★ 5.2k • written 6.5 years ago by • 0
2
votes
4
replies
1.6k
views
Are there any functions to subtract all features(rows) to a particular value(row) in the same data file?
R python normalization matrix
updated 6.3 years ago by ▴ 30 • written 6.3 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Job: Bioinformatics Analyst II, Genomics Shared Resource (Seattle, WA)
GENOMICS BIOINFORMATICS SEATTLE R PYTHON Job
6.3 years ago Fred Hutch (Recruiting) ▴ 40
1
vote
2
replies
1.2k
views
Support for import of custom matrix data in the ddCt R package
ddCt import analysis R qRTPCR
updated 6.3 years ago by ▴ 120 • written 6.3 years ago by ▴ 10
1,163 results • Page 7 of 24
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Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by aqeel • 0
Discover the pinnacle of Brazilian Jiu Jitsu gear at [Dragon][1] GI. [1]: https://dragongi.com/
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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