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0
votes
3
replies
212
views
Biomart issue, why so few 3'utrs?
utr biomart
updated 3 days ago by 142k • written 4 days ago by ▴ 270
0
votes
1
reply
176
views
sorted bam file generated from gff transcript fastas, how to get counts with HTseq?
htseq bam
updated 6 weeks ago by 43k • written 6 weeks ago by ▴ 270
0
votes
1
reply
183
views
mirbase gff and mature fastas for custom STAR index genome?
mirbase indexing star genome
6 weeks ago by RNAseqer ▴ 270
3
votes
4
replies
696
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR volcano plotting R plot
updated 5 months ago by ★ 1.6k • written 5 months ago by ▴ 270
1
vote
2
replies
1.9k
views
junction_annotation.py: How many 'novel' splice junctions/splice events are resonably expected from human RNA,
RNA-Seq junction_annotation.py human
updated 8 months ago by ▴ 20 • written 5.3 years ago by ▴ 270
2
votes
1
reply
830
views
coef /makeContrasts very different results
makeContrasts coef2 edgeR
updated 12 months ago by ★ 7.2k • written 13 months ago by ▴ 270
0
votes
1
reply
925
views
mirge3.0 custom miRNA db option
database custom miRNA mirge3.0
updated 15 months ago by • 0 • written 2.9 years ago by ▴ 270
6
votes
2
replies
1.8k
views
WGCNA: outputting multiple hubgenes from a module
WGCNA HubGenes
updated 21 months ago by ▴ 30 • written 4.0 years ago by ▴ 270
0
votes
0
replies
347
views
custom sizing question in ggseqlogo. sequence logo creation
logo sequence R ggseqlogo
23 months ago by RNAseqer ▴ 270
0
votes
0
replies
358
views
geo database for integrated miRNA-mRNA sequencing of neural cell
mir-seq mrna-seq
2.2 years ago by RNAseqer ▴ 270
0
votes
0
replies
326
views
How to get a screeplot of surrogate variables from sva()
screeplot sva svaseq
2.2 years ago by RNAseqer ▴ 270
0
votes
0
replies
623
views
WGCNA, module preservation over permutations, how to?
module WGCNA preservation
2.4 years ago by RNAseqer ▴ 270
0
votes
0
replies
416
views
what regression model does step() in R use
lm function R model stepwise
2.5 years ago by RNAseqer ▴ 270
0
votes
1
reply
857
views
How to extract beta coefficients from edgeR output
rnaseq beta coefficient r edger
updated 2.5 years ago by ★ 7.2k • written 2.6 years ago by ▴ 270
2
votes
1
reply
585
views
EdgeR exclude 0 count subjects for each gene
count edgeR R
updated 2.5 years ago by ★ 7.2k • written 2.5 years ago by ▴ 270
0
votes
0
replies
477
views
How do you convert vcf file to a genotype file useable by eigenstrat
conversion vcf format eigenstrat
2.6 years ago by RNAseqer ▴ 270
0
votes
0
replies
575
views
accessing the r-peer docker container.
docker peer r
2.6 years ago by RNAseqer ▴ 270
0
votes
1
reply
616
views
Analysis of a SNPs moderating effect on disease
effect SNP moderating
updated 2.6 years ago by 6.4k • written 2.6 years ago by ▴ 270
5
votes
2
replies
935
views
Most well regarded piRNA detection pipeline/program
expression piRNA differential smallRNAseq detection
2.6 years ago by RNAseqer ▴ 270
0
votes
0
replies
452
views
how to identiify real isomers in mirge3.0's output files.
isomirs mirge3.0
2.7 years ago by RNAseqer ▴ 270
0
votes
0
replies
891
views
REditools2 (HPC-reditools) de-novo editing prediction from RNAseq?
editing reditools2 prediction RNAseq
2.7 years ago by RNAseqer ▴ 270
0
votes
3
replies
880
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 2.8 years ago by 82k • written 2.8 years ago by ▴ 270
0
votes
0
replies
472
views
Can you get individual sample counts from Spar (Small RNA-seq portal for analysis of sequencing experiments)
Differential RNAseq SPAR Expression
3.0 years ago by RNAseqer ▴ 270
0
votes
0
replies
513
views
getting residuals from dream
dream limma residuals
3.1 years ago by RNAseqer ▴ 270
0
votes
0
replies
517
views
limma dream giving error message 'subscript out of bounds'
error Dream R
3.1 years ago by RNAseqer ▴ 270
0
votes
0
replies
814
views
alternative package for littlesMCAR() or mcar_test()
littlesMCAR MCAR missingdata
3.1 years ago by RNAseqer ▴ 270
5
votes
2
replies
845
views
Heirarchal regression for model comparison, RNA-seq
R RNA-seq heirarchalregression
updated 3.2 years ago by 82k • written 3.2 years ago by ▴ 270
1
vote
5
replies
1.4k
views
chi squared assesment of gene expression and batch effect
RNA-Seq r chi squared
3.2 years ago by RNAseqer ▴ 270
0
votes
1
reply
823
views
model matrix error message 'unequal columns/rows' when using a conditional variable
rna-seq categorical variables edger
updated 3.2 years ago by ★ 7.2k • written 3.2 years ago by ▴ 270
0
votes
1
reply
619
views
Nesting a covariate for differential expression design
RNA-Seq nested covariates
updated 3.2 years ago by 20 • written 3.2 years ago by ▴ 270
1
vote
1
reply
682
views
voomWithDreamWeights() has missing "NA" wheights for last samples
voomWithDreamWeights dream variaincePartition
3.2 years ago by RNAseqer ▴ 270
3
votes
4
replies
3.2k
views
GSEA pvalue output of 0.0. Can I make it more specific?
GSEA P-value
updated 3.2 years ago by ▴ 930 • written 3.8 years ago by ▴ 270
9
votes
4
replies
4.9k
views
A question regarding log2 transformation in EdgeR
EdgeR log2 differentail expression analysis
updated 3.2 years ago by ★ 7.2k • written 3.2 years ago by ▴ 270
0
votes
0
replies
590
views
package for ICC plots from a matrix?
ICC plots R
3.3 years ago by RNAseqer ▴ 270
2
votes
4
replies
776
views
Is miarma-Seq being maintained?
miarma-Seq miRNA RNA-Seq
3.5 years ago by RNAseqer ▴ 270
0
votes
0
replies
564
views
best practices/ pipeline for miRNA sequencing QC
RNA-Seq miRNA-seq QC
3.5 years ago by RNAseqer ▴ 270
0
votes
1
reply
1.0k
views
Is there a good reference matrix for miRNA array deconvolution?
miRNA microarray deconvolution
updated 3.8 years ago by • 0 • written 4.1 years ago by ▴ 270
0
votes
1
reply
647
views
constructing a reference matrix from affy 2.0 chip for a 4.0 chip.
affy miRNA Affymetrix Multispecies miRNA-1 Array
4.0 years ago by RNAseqer ▴ 270
3
votes
2
replies
2.0k
views
affy Transcriptome Analysis Console (TAC), export expression matrix?
affy TAC expression matrix
4.1 years ago by RNAseqer ▴ 270
1
vote
2
replies
728
views
Small number of genes, drop in sft fit curve at higher threshold powers. why?
sft wgcna scale-free
updated 4.1 years ago by 88k • written 4.1 years ago by ▴ 270
3
votes
3
replies
1.1k
views
Excel: using quartiles & averageifs to combine probe values without outliers
excel outliers quartile averageifs matching
updated 4.2 years ago by 14k • written 4.2 years ago by ▴ 270
4
votes
4
replies
1.6k
views
A good place to get immune cell deconvolution reference datasets?
deconvolution reference datasets
updated 4.3 years ago by ★ 16k • written 4.3 years ago by ▴ 270
3
votes
3
replies
1.6k
views
Correlating WGCNA modules to Diseased/Not-Diseased Trait
WGCNA Modules Traits
updated 4.7 years ago by 3.6k • written 4.7 years ago by ▴ 270
0
votes
1
reply
992
views
extracting a subset of probes from an expression object
subset probes microarray exprs
updated 4.8 years ago by 20 • written 5.0 years ago by ▴ 270
1
vote
1
reply
5.2k
views
how to adjust for continuous covariates in limma?
limma continuous covariates DE
updated 4.9 years ago by 19k • written 4.9 years ago by ▴ 270
0
votes
0
replies
576
views
summarized probes with expresso. how do i get transcript IDs?
affy expresso transcript ID
4.9 years ago by RNAseqer ▴ 270
0
votes
0
replies
882
views
is there an function to summarize miRNA array probes but do nothing else?
summarise probes affy miRNA
4.9 years ago by RNAseqer ▴ 270
2
votes
5
replies
2.3k
views
changing feature names (row names) for expressionset object?
expressionset limma rownames
5.0 years ago by RNAseqer ▴ 270
0
votes
0
replies
890
views
whats is the best normalization technique for miRNA microarray data?
normalization miRNA microarray
5.0 years ago by RNAseqer ▴ 270
6
votes
4
replies
3.0k
views
pData function not found. substitute? "An end to end workflow for differential gene expression using Affymetrix microarrays"
pvca bioconductor sva pData R
updated 5.0 years ago by 11k • written 5.0 years ago by ▴ 270
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