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0
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0
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1.0k
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Estimating sample size for specific platforms
software error RnaSeqSampleSize r RNA-seq
6.5 years ago AZ ▴ 30
0
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0
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1.1k
views
Job: Data science research assistant position at Johns Hopkins
RNAseq R Next-Gen Sequencing Imaging Brain Job
6.5 years ago hjaarop1 • 0
0
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0
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2.3k
views
Error in contrasts<-(tmp, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels
software error ballgown rstudio R stattest
6.5 years ago fatimarasool135 • 0
0
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0
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1.6k
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
6.5 years ago gerald.mccollam • 0
7
votes
3
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4.5k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 10
2
votes
6
replies
2.7k
views
featurecounts Rsubread ERROR on exon_id
R error software error Rsubread featurecounts
updated 6.5 years ago by ★ 3.6k • written 6.5 years ago by • 0
0
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0
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1.2k
views
Job: Summer Studentships in Data Science & Computational Biology (2019) at the University of Cambridge
R Python Computational-Biology Cancer Job
6.5 years ago Shamith.Samarajiwa ▴ 180
2
votes
2
replies
1.2k
views
Where can I get functional bins for Arabidopsis thaliana genome (AGIs)
r proteomics RNA-Seq
updated 6.5 years ago by ▴ 180 • written 6.5 years ago by ▴ 10
0
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0
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1.1k
views
How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r metabolomics KEGG Proteomics Transcriptomics
6.5 years ago Wuschel ▴ 10
0
votes
6
replies
1.7k
views
RSBML wrong edges
rsbml R CellDesigner
updated 6.5 years ago by ★ 11k • written 6.6 years ago by • 0
0
votes
1
reply
1.3k
views
Submitting R package in Bioconductor with Plink and vcftools Dependencies
R package dependencies
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
0
votes
7
replies
2.5k
views
GO.db installation problems with BiocManager in R
R Bioconductor
6.6 years ago d.m.j.thorburn • 0
2
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3
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2.0k
views
bplapply - only SerialParam or single worker Multicore working on R/macos 10.14
BiocParallel mac R
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 10
1
vote
3
replies
1.8k
views
Obtain coordinates of 5' upstream region up to closest coding region
r granges promoter
updated 6.6 years ago by 16k • written 6.6 years ago by • 0
0
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2
replies
1.0k
views
using limma for circular RNA analyses
limma R edger
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
0
votes
1
reply
910
views
Getting a signature specific to each patient
DESeq2 r cancer
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 30
2
votes
1
reply
1.2k
views
Error in reading sbml file
rsbml R
updated 6.6 years ago by ★ 11k • written 6.6 years ago by • 0
7
votes
3
replies
6.0k
views
VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
r limma voom vsn
updated 2.9 years ago by 53k • written 6.6 years ago by ▴ 70
0
votes
1
reply
2.4k
views
Multiple R versions
R bioc
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
0
votes
5
replies
2.9k
views
Getting opposite log2 fold change
deseq2 gene expression log2foldchange R
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
2
votes
1
reply
1.8k
views
Create a matrix to show overlaps among multiple GRanges
r GRanges GenomicRanges
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 40
0
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0
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900
views
Multiple alignment solution for a character object of short fragments
r alignment
6.6 years ago r.tor • 0
3
votes
3
replies
2.8k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 6.6 years ago by ★ 3.0k • written 6.6 years ago by ▴ 60
5
votes
10
replies
3.1k
views
caught segfault error when loading S4Vectors package in R
R S4Vectors segfault
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 30
3
votes
1
reply
1.7k
views
What is the "linear model" part used for in Limma?
Limma R Linear Models
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
2
votes
1
reply
719
views
Iterate through sever annotation database packages
R annotation
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
1
vote
2
replies
917
views
Microarray Analysis of Sleep Deprivation Data Experimental Design
limma gene expression r diffeential expression microarray analysis
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
0
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0
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768
views
Error while using COHCAP pipeline for 450k methylation data analysis
r cohcap 450k methylation
6.7 years ago sayamsmruti • 0
1
vote
3
replies
801
views
How do you obtain the R - squared value from the NB line produced in plotMeanVar ?
edger rnaseq R
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
0
votes
2
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6.7k
views
[Resolved] RcppArmadillo pckg ERRORS : non-zero exit status (and so DESeq2 also)
DESEq2 R linux RcppArmadillo
6.7 years ago RS1 • 0
0
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0
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1.6k
views
OpenBLAS issue with ComBat() function of the R SVA package on Torque cluster
sva R OpenBLAS
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
0
votes
0
replies
955
views
How to merging multiple GSEs with different GPLs?
microarray probe R
6.7 years ago maryam.sabet • 0
0
votes
1
reply
897
views
Paired samples in DESeq2
R deseq2 Paired Samples
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
votes
1
reply
2.1k
views
WGCNA soft threshold power showing very strange values
wgcna soft threshold r scale independence scale free topology model fit
updated 6.7 years ago by ★ 3.0k • written 6.7 years ago by • 0
0
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2
replies
3.4k
views
DESEq2 rownames: NULL
deseq2 R
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
2
votes
5
replies
2.3k
views
edgeR or wilcoxon rank test? Which is right?
edgeR r wilcox RNA-seq cancer
6.7 years ago AZ ▴ 30
2
votes
1
reply
3.2k
views
Selection of terms in clusterProfiler, the inverse of dropGO
clusterProfiler r
6.7 years ago Sebastian Hesse ▴ 70
5
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6
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4.4k
views
error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 6.7 years ago by 16k • written 6.7 years ago by • 0
2
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3
replies
1.3k
views
Batch correction for a sets of genes
cancer deseq2 r rnaseq
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 30
4
votes
4
replies
2.8k
views
Matching GenBank Accession Number with corresponding Biomart results
annotation biomaRt r
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
5
votes
10
replies
5.3k
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
2
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4
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1.1k
views
Dealing with HSP in blast output with GRanges
GRangers R
updated 6.7 years ago by 25k • written 6.7 years ago by • 0
0
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2
replies
6.6k
views
Converting Fastq to Fasta in R
R Bioinformatics Fastq Fasta
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
0
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0
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1.0k
views
R: estimating error rate of replicated samples
R SNP genotyping genetic diversity
6.7 years ago meriam.nef • 0
3
votes
7
replies
1.7k
views
Limma analysis, controlling for Donors.
limma r microarray
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
0
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0
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759
views
R ArrayExpress probleme
R
6.8 years ago hafidimustapha • 0
0
votes
1
reply
1.5k
views
Meta_analysis of different platforms of microarray data
microarray meta analysis cancer Software R
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
2
votes
2
replies
2.4k
views
Array Normalization on focussed array in Limma using R
limma microarray r
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
0
votes
1
reply
1.3k
views
Biseq installation error
biseq package installation r
updated 6.8 years ago by 25k • written 6.8 years ago by • 0
0
votes
0
replies
980
views
Superheat adjusting making left label size
r R heatmap
6.8 years ago coyoung ▴ 10
1,163 results • Page 9 of 24
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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…
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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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