Showing : R • reset
2
votes
4
replies
1.9k
views
Impose minimum restrictions on correlations in SingleR
single cell R SingleR
updated 5.7 years ago by ★ 29k • written 5.7 years ago by ▴ 120
5
votes
1
reply
4.3k
views
How to translate FASTA file of DNA sequence to protein sequence using Biostrings package?
Biostrings Bioconductor R
updated 5.8 years ago by ▴ 110 • written 5.8 years ago by ▴ 20
0
votes
2
replies
1.2k
views
keggLink Error: linking "genes" and "reaction"
software error keggLink R
updated 5.8 years ago by 4.2k • written 5.8 years ago by • 0
0
votes
1
reply
1.4k
views
boxplot Error in Bioconductor
boxplot bioconductor R error
5.8 years ago l154359 • 0
1
vote
1
reply
1.1k
views
model matrix in limma
limma R
updated 5.8 years ago by 53k • written 5.8 years ago by ▴ 40
1
vote
1
reply
14k
views
Install Bioconductor in R studio
R
updated 5.8 years ago by ★ 4.0k • written 5.8 years ago by • 0
0
votes
1
reply
1.1k
views
CNV plot using cn.mops
cnv R plot visualization cn.mops software error
5.8 years ago ari • 0
0
votes
0
replies
1.6k
views
Job: Postdoc and PhD student in Bioinformatics/Biostatistics
NGS R statistics genomics big data Job
6.7 years ago • updated 5.9 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 5.9 years ago by ★ 1.4k • written 5.9 years ago by ▴ 30
4
votes
4
replies
2.8k
views
How I interpret this plot from pathview
pathview kegg r pathway
5.9 years ago AZ ▴ 30
1
vote
10
replies
11k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 11 weeks ago by 43k • written 5.9 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
5.9 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
5.9 years ago info ▴ 10
0
votes
5
replies
2.4k
views
readTranscriptFeatures from genomation
R Rstudio Error readTranscriptFeatures genomation
updated 5.9 years ago by ▴ 20 • written 5.9 years ago by • 0
1
vote
1
reply
2.4k
views
uploading xml file in flowworkspace
flowworkspace xml R flowjo
updated 5.9 years ago by • 0 • written 8.6 years ago by ▴ 10
3
votes
6
replies
6.4k
views
WGCNA gene significance and module membership
WGCNA R
updated 2.9 years ago by ★ 3.0k • written 5.9 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
5.9 years ago wang.lingjue • 0
2
votes
0
replies
1.1k
views
SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
5.9 years ago rmash ▴ 20
0
votes
1
reply
1.2k
views
plotEigengeneNetworks WGCNA add ME labels to left side of figure
R WGCNA
5.9 years ago normingt • 0
0
votes
3
replies
1.4k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 6.0 years ago by 25k • written 6.0 years ago by • 0
1
vote
3
replies
1.5k
views
How can I run a paired RankProd analysis in R?
RankProd paired RNAseq R
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
4
votes
5
replies
1.3k
views
Defining the design for a complicated multi-level experiment in Limma
limma RNASeq R voom
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 60
2
votes
1
reply
11k
views
Error: status was 'SSL connect error'
bioconductor proxy macOS R RStudio
updated 6.0 years ago by 25k • written 6.0 years ago by ▴ 20
1
vote
1
reply
1.5k
views
Gviz UCSC tracks not visible
Gviz R UCSC Tracks genome locusplot
updated 6.0 years ago by ▴ 750 • written 6.0 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 6.0 years ago by 25k • written 6.0 years ago by • 0
0
votes
0
replies
984
views
Unable to obtain the line chart with error envelop in ggplot2 and geom_ribbon()
ggplot2 line chart R geom_ribbon()
6.0 years ago mohammedtoufiq91 ▴ 10
5
votes
8
replies
2.6k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 6.0 years ago by ★ 13k • written 6.0 years ago by ▴ 30
0
votes
0
replies
1.0k
views
Job: Bioinformatician @ University of Cambridge
cancer bioinformatics R Job
6.0 years ago Shamith.Samarajiwa ▴ 180
0
votes
3
replies
678
views
DESeq2 Identical P values in both standard and multi factor design
deseq2 r
6.0 years ago dtlloyd • 0
2
votes
2
replies
4.4k
views
How adjusted p-values are calculated in limma
limma r transcriptomics FDR statistics
updated 6.0 years ago by 53k • written 6.0 years ago by ▴ 10
2
votes
2
replies
644
views
Order of design matrix for edgeR analysis
edger r
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
0
votes
0
replies
1.2k
views
Output GenVisR mutation frequency data by gene name instead of by sample name
GenVisR mutation frequency R cancer bioconductor
6.1 years ago sheneicechang • 0
1
vote
1
reply
1.2k
views
Querying CTD database to find diseases associated with the given pathways.
CTD Database disease pathway association R programming
6.1 years ago omarrafiqued ▴ 50
2
votes
1
reply
725
views
ImportFrom statement in package
R
updated 6.1 years ago by 68k • written 6.1 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 6.1 years ago by ★ 6.6k • written 6.1 years ago by ▴ 60
3
votes
7
replies
4.4k
views
Handle missing values in the z-score matrix while plotting heatmap in the ComplexHeatmap
matrix heatmap ComplexHeatmap missing values R
updated 6.1 years ago by ▴ 290 • written 6.1 years ago by ▴ 10
0
votes
0
replies
914
views
News: Protemics with R and Bioconductor course in Berlin
R Proteomics News
6.1 years ago info ▴ 10
4
votes
3
replies
5.1k
views
Differential gene expression anlaysis?
rnaseq R normalization
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 30
0
votes
5
replies
1.6k
views
Does anyone have experience using the massiR package?
massiR microarray R probe
6.1 years ago Steve Lowe ▴ 30
0
votes
2
replies
888
views
Combining different arrays in analysis
array R normalization
updated 6.1 years ago by 68k • written 6.1 years ago by ▴ 30
4
votes
9
replies
2.3k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
1
vote
4
replies
2.4k
views
Merging two files based on the identifier column (gene symbols)?
merge files R packages gene annotations
6.1 years ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
1.1k
views
News: R/Bioconductor for Mass Spectrometry and Proteomics course in Berlin
Bioconductor R News
6.1 years ago info ▴ 10
0
votes
1
reply
1.5k
views
Installation problem in IlluminaHumanMethylation450kanno.ilmn12.hg19
IlluminaHumanMethylation450kanno.ilmn12.hg19 R
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
1
vote
1
reply
1.1k
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 6.1 years ago by 43k • written 6.1 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
6.1 years ago sabrina.mcnew • 0
0
votes
1
reply
1.9k
views
DiffBind dba error
DiffBind dba R error
updated 6.1 years ago by ★ 5.2k • written 6.3 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 6.2 years ago by ▴ 30 • written 6.2 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Job: Bioinformatics Analyst II, Genomics Shared Resource (Seattle, WA)
GENOMICS BIOINFORMATICS SEATTLE R PYTHON Job
6.2 years ago Fred Hutch (Recruiting) ▴ 40
1
vote
2
replies
1.1k
views
Support for import of custom matrix data in the ddCt R package
ddCt import analysis R qRTPCR
updated 6.2 years ago by ▴ 120 • written 6.2 years ago by ▴ 10
1,163 results • Page 7 of 24
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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