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1
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456
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Comment: Comment: samtools version 1.17 having difficulty parsing a filtering command. advice?
7 weeks ago by RNAseqer ▴ 280
1
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3
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456
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samtools version 1.17 having difficulty parsing a filtering command. advice?
samtools cell rnaseq single
updated 7 weeks ago by ▴ 350 • written 7 weeks ago by ▴ 280
0
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3
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516
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Biomart issue, why so few 3'utrs?
utr biomart
updated 8 months ago by 148k • written 8 months ago by ▴ 280
0
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0
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409
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Comment: Comment: mirbase gff and mature fastas for custom STAR index genome?
9 months ago by RNAseqer ▴ 280
0
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1
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344
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sorted bam file generated from gff transcript fastas, how to get counts with HTseq?
htseq bam
updated 9 months ago by 44k • written 9 months ago by ▴ 280
0
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1
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409
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mirbase gff and mature fastas for custom STAR index genome?
mirbase indexing star genome
9 months ago by RNAseqer ▴ 280
0
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2
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1.2k
views
Comment: Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
13 months ago by RNAseqer ▴ 280
3
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4
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1.2k
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Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR volcano plotting R plot
updated 13 months ago by ★ 1.6k • written 13 months ago by ▴ 280
1
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2
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2.1k
views
junction_annotation.py: How many 'novel' splice junctions/splice events are resonably expected from human RNA,
RNA-Seq junction_annotation.py human
updated 16 months ago by ▴ 20 • written 5.9 years ago by ▴ 280
2
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1
reply
1.1k
views
coef /makeContrasts very different results
makeContrasts coef2 edgeR
updated 20 months ago by ★ 7.8k • written 21 months ago by ▴ 280
0
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1
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1.0k
views
mirge3.0 custom miRNA db option
database custom miRNA mirge3.0
updated 23 months ago by • 0 • written 3.6 years ago by ▴ 280
6
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2
replies
2.0k
views
WGCNA: outputting multiple hubgenes from a module
WGCNA HubGenes
updated 2.5 years ago by ▴ 30 • written 4.6 years ago by ▴ 280
0
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0
replies
426
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custom sizing question in ggseqlogo. sequence logo creation
logo sequence R ggseqlogo
2.6 years ago by RNAseqer ▴ 280
0
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0
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419
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geo database for integrated miRNA-mRNA sequencing of neural cell
mir-seq mrna-seq
2.9 years ago by RNAseqer ▴ 280
0
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0
replies
397
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How to get a screeplot of surrogate variables from sva()
screeplot sva svaseq
2.9 years ago by RNAseqer ▴ 280
0
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0
replies
728
views
WGCNA, module preservation over permutations, how to?
module WGCNA preservation
3.1 years ago by RNAseqer ▴ 280
0
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0
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10k
views
Comment: Comment: convert from plink format into 012 format
3.1 years ago by RNAseqer ▴ 280
0
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0
replies
508
views
what regression model does step() in R use
lm function R model stepwise
3.2 years ago by RNAseqer ▴ 280
0
votes
1
reply
998
views
How to extract beta coefficients from edgeR output
rnaseq beta coefficient r edger
updated 3.2 years ago by ★ 7.8k • written 3.3 years ago by ▴ 280
2
votes
1
reply
713
views
EdgeR exclude 0 count subjects for each gene
count edgeR R
updated 3.2 years ago by ★ 7.8k • written 3.2 years ago by ▴ 280
0
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0
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566
views
How do you convert vcf file to a genotype file useable by eigenstrat
conversion vcf format eigenstrat
3.2 years ago by RNAseqer ▴ 280
0
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0
replies
654
views
accessing the r-peer docker container.
docker peer r
3.2 years ago by RNAseqer ▴ 280
0
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1
reply
740
views
Analysis of a SNPs moderating effect on disease
SNP moderating-effect
updated 5 months ago by 44k • written 3.3 years ago by ▴ 280
0
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0
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1.1k
views
Comment: Comment: Most well regarded piRNA detection pipeline/program
3.3 years ago by RNAseqer ▴ 280
5
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2
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1.1k
views
Most well regarded piRNA detection pipeline/program
expression piRNA differential smallRNAseq detection
3.3 years ago by RNAseqer ▴ 280
0
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0
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538
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how to identiify real isomers in mirge3.0's output files.
isomirs mirge3.0
3.3 years ago by RNAseqer ▴ 280
0
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0
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1.0k
views
REditools2 (HPC-reditools) de-novo editing prediction from RNAseq?
editing reditools2 prediction RNAseq
3.4 years ago by RNAseqer ▴ 280
0
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1
reply
1000
views
Comment: Comment: what is the best R package/function to perform an Equality of variance F-test on
3.5 years ago by RNAseqer ▴ 280
0
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3
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1000
views
what is the best R package/function to perform an Equality of variance F-test on TMM log2 gene expression values
gene-expression F-test equality-of-variance
updated 3.5 years ago by 86k • written 3.5 years ago by ▴ 280
0
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0
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531
views
Can you get individual sample counts from Spar (Small RNA-seq portal for analysis of sequencing experiments)
Differential RNAseq SPAR Expression
3.7 years ago by RNAseqer ▴ 280
0
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0
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605
views
getting residuals from dream
dream limma residuals
3.7 years ago by RNAseqer ▴ 280
0
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0
replies
591
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limma dream giving error message 'subscript out of bounds'
error Dream R
3.8 years ago by RNAseqer ▴ 280
0
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0
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949
views
alternative package for littlesMCAR() or mcar_test()
littlesMCAR MCAR missingdata
3.8 years ago by RNAseqer ▴ 280
5
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2
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974
views
Heirarchal regression for model comparison, RNA-seq
R RNA-seq heirarchalregression
updated 3.8 years ago by 86k • written 3.8 years ago by ▴ 280
0
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0
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1.7k
views
Comment: Comment: chi squared assesment of gene expression and batch effect
3.8 years ago by RNAseqer ▴ 280
1
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5
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1.7k
views
chi squared assesment of gene expression and batch effect
RNA-Seq r chi squared
3.8 years ago by RNAseqer ▴ 280
0
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1
reply
1.0k
views
model matrix error message 'unequal columns/rows' when using a conditional variable
rna-seq categorical variables edger
updated 3.8 years ago by ★ 7.8k • written 3.9 years ago by ▴ 280
0
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1
reply
711
views
Nesting a covariate for differential expression design
RNA-Seq nested covariates
updated 3.8 years ago by 20 • written 3.9 years ago by ▴ 280
0
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1
reply
1.7k
views
Comment: C: chi squared assesment of gene expression and batch effect
3.8 years ago by RNAseqer ▴ 280
1
vote
1
reply
804
views
voomWithDreamWeights() has missing "NA" wheights for last samples
voomWithDreamWeights dream variaincePartition
3.9 years ago by RNAseqer ▴ 280
1
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0
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804
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Answer: A: voomWithDreamWeights() has missing "NA" wheights for last samples
3.9 years ago by RNAseqer ▴ 280
3
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4
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3.8k
views
GSEA pvalue output of 0.0. Can I make it more specific?
GSEA P-value
updated 3.9 years ago by ▴ 1000 • written 4.5 years ago by ▴ 280
0
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0
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6.1k
views
Comment: C: A question regarding log2 transformation in EdgeR
3.9 years ago by RNAseqer ▴ 280
10
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4
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6.1k
views
A question regarding log2 transformation in EdgeR
EdgeR log2 differentail expression analysis
updated 3.9 years ago by ★ 7.8k • written 3.9 years ago by ▴ 280
0
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1
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6.1k
views
Comment: C: A question regarding log2 transformation in EdgeR
3.9 years ago by RNAseqer ▴ 280
0
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0
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681
views
package for ICC plots from a matrix?
ICC plots R
4.0 years ago by RNAseqer ▴ 280
0
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0
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897
views
Comment: C: Is miarma-Seq being maintained?
4.1 years ago by RNAseqer ▴ 280
2
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4
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897
views
Is miarma-Seq being maintained?
miarma-Seq miRNA RNA-Seq
4.1 years ago by RNAseqer ▴ 280
0
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0
replies
651
views
best practices/ pipeline for miRNA sequencing QC
RNA-Seq miRNA-seq QC
4.2 years ago by RNAseqer ▴ 280
0
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1
reply
1.1k
views
Is there a good reference matrix for miRNA array deconvolution?
miRNA microarray deconvolution
updated 4.5 years ago by • 0 • written 4.7 years ago by ▴ 280
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