Showing : r • reset
2
votes
4
replies
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
6.8 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 6.0 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 • updated 6.0 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 6.0 years ago by • 0
0
votes
2
replies
2.4k
views
How to adjust and align timepoints on x-axis in the ggplot2
ggplot2 line plot x-axis data frame R
6.0 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
6.4k
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
2.6k
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 6.1 years ago by 68k • written 6.1 years ago by ▴ 60
2
votes
1
reply
11k
views
Error: status was 'SSL connect error'
bioconductor proxy macOS R RStudio
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 20
1
vote
1
reply
1.6k
views
Gviz UCSC tracks not visible
Gviz R UCSC Tracks genome locusplot
updated 6.1 years ago by ▴ 750 • written 6.1 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
726
views
DESeq2 Identical P values in both standard and multi factor design
deseq2 r
6.2 years ago dtlloyd • 0
2
votes
2
replies
4.5k
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
677
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
755
views
ImportFrom statement in package
R
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
2
votes
6
replies
1.7k
views
Can't install GOSEQ (dependency problem) on CentOS 7!
goseq r package r
updated 6.2 years ago by ★ 6.6k • written 6.2 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 6.2 years ago by ▴ 290 • written 6.2 years ago by ▴ 10
0
votes
0
replies
944
views
News: Protemics with R and Bioconductor course in Berlin
R Proteomics News
6.2 years ago info ▴ 10
4
votes
3
replies
5.2k
views
Differential gene expression anlaysis?
rnaseq R normalization
updated 6.2 years ago by 53k • written 6.2 years ago by ▴ 30
0
votes
5
replies
1.7k
views
Does anyone have experience using the massiR package?
massiR microarray R probe
6.3 years ago Steve Lowe ▴ 30
0
votes
2
replies
989
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
2.9k
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
Recent ...
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Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
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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