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1
vote
5
replies
5.8k
views
How to in R: Include principal components as covariates in analysis
pca covariates principal components
updated 5.0 years ago by 87k • written 5.0 years ago by ▴ 270
3
votes
1
reply
682
views
batchCombat package for R?
batchCombat R
updated 5.0 years ago by 82k • written 5.0 years ago by ▴ 270
3
votes
3
replies
2.5k
views
Principal component analysis of SVA's surrogate variables
sva stdev surrogate variables
updated 5.0 years ago by 12k • written 5.0 years ago by ▴ 270
0
votes
1
reply
1.6k
views
contrast matrix design question, limma-sva
contrast matrix sva limma
5.0 years ago by RNAseqer ▴ 270
0
votes
0
replies
1.0k
views
sva pprob.b all 0s?
sva microarray r pprob.b
5.0 years ago by RNAseqer ▴ 270
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 24 days ago by 43k • written 5.0 years ago by ▴ 270
7
votes
3
replies
7.4k
views
how do you remove the trace in heatmap.2 in R?
heatmap.2 r microarray heat map
updated 5.0 years ago by 87k • written 5.0 years ago by ▴ 270
2
votes
2
replies
1.3k
views
limma, best practices review paper?
R limma microarray
updated 5.0 years ago by 87k • written 5.0 years ago by ▴ 270
0
votes
2
replies
925
views
minimum snp number from set in LD
snps ld minimum snp number
updated 5.1 years ago by ★ 1.4k • written 5.1 years ago by ▴ 270
15
votes
2
replies
8.6k
views
pulling snps from vcf file using ids
vcf ids snps
updated 5.1 years ago by 87k • written 5.1 years ago by ▴ 270
1
vote
1
reply
1.9k
views
Default Plink Window size?
plink window SNP
updated 5.1 years ago by 87k • written 5.1 years ago by ▴ 270
2
votes
3
replies
1.7k
views
Plink recode option to get genomic position?
plink SNP locus
updated 5.1 years ago by 11k • written 5.1 years ago by ▴ 270
8
votes
10
replies
2.7k
views
Interpreting plink snp tagging output
plink SNP
updated 5.1 years ago by 10k • written 5.1 years ago by ▴ 270
3
votes
2
replies
5.3k
views
Filtering SNPS by minimum LD value in bcftools?
bcftools vcftools vcf LD r2
5.1 years ago by RNAseqer ▴ 270
12
votes
5
replies
5.0k
views
rowVars function, used in ballgown analysis not available for R 3.5.2, alternatives?
R rna-seq ballgown rowVars
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 270
0
votes
4
replies
2.8k
views
ballgown error: Error in file(file, "rt") : invalid 'description' argument Calls: ballgown -> read.table -> file
ballgown RNA-Seq stringtie
5.2 years ago by RNAseqer ▴ 270
0
votes
2
replies
2.4k
views
No Sensitivity/Accuracy output from gffcompare, what am I doing wrong?
gffcompare .stats. accuracy precision
5.2 years ago by RNAseqer ▴ 270
1
vote
1
reply
1.5k
views
Can HISAT2 be invoked in bash shell, and can it be fed variables or names with wildcards as inputs?
Bash Shell HISAT2
updated 11 months ago by 43k • written 5.2 years ago by ▴ 270
2
votes
7
replies
2.7k
views
samtools sam-to-bam conversion => bamfile RSeQC tool bam_stats.py cannot use. ValueError: file has no sequences defined (mode='rb')
samtools bam RSeQC bam_stats.py (mode='rb')
updated 5.2 years ago by 47k • written 5.2 years ago by ▴ 270
0
votes
4
replies
3.0k
views
Hisat2 -Can it align paired readfiles, and unpaired read files leftover from trimming/QC simultaneously?
rna-seq alignment HISAT2 Paired end
updated 5.2 years ago by 35k • written 5.2 years ago by ▴ 270
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