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0
votes
1
reply
153
views
sorted bam file generated from gff transcript fastas, how to get counts with HTseq?
htseq
bam
updated 21 days ago by
Ram
43k • written 21 days ago by
RNAseqer
▴ 260
0
votes
1
reply
158
views
mirbase gff and mature fastas for custom STAR index genome?
mirbase
indexing
star
genome
21 days ago by
RNAseqer
▴ 260
3
votes
4
replies
611
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 4 months ago by
Nitin Narwade
★ 1.6k • written 4 months ago by
RNAseqer
▴ 260
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 7 months ago by
Nicolas Lichilin
▴ 20 • written 5.2 years ago by
RNAseqer
▴ 260
2
votes
1
reply
806
views
coef /makeContrasts very different results
makeContrasts
coef2
edgeR
updated 11 months ago by
Gordon Smyth
★ 7.0k • written 12 months ago by
RNAseqer
▴ 260
0
votes
1
reply
911
views
mirge3.0 custom miRNA db option
database
custom
miRNA
mirge3.0
updated 14 months ago by
arun
• 0 • written 2.8 years ago by
RNAseqer
▴ 260
6
votes
2
replies
1.8k
views
WGCNA: outputting multiple hubgenes from a module
WGCNA
HubGenes
updated 21 months ago by
tiancaigg
▴ 30 • written 3.9 years ago by
RNAseqer
▴ 260
0
votes
0
replies
339
views
custom sizing question in ggseqlogo. sequence logo creation
logo
sequence
R
ggseqlogo
23 months ago by
RNAseqer
▴ 260
0
votes
0
replies
351
views
geo database for integrated miRNA-mRNA sequencing of neural cell
mir-seq
mrna-seq
2.1 years ago by
RNAseqer
▴ 260
0
votes
0
replies
317
views
How to get a screeplot of surrogate variables from sva()
screeplot
sva
svaseq
2.1 years ago by
RNAseqer
▴ 260
0
votes
0
replies
610
views
WGCNA, module preservation over permutations, how to?
module
WGCNA
preservation
2.4 years ago by
RNAseqer
▴ 260
0
votes
0
replies
402
views
what regression model does step() in R use
lm
function
R
model
stepwise
2.4 years ago by
RNAseqer
▴ 260
0
votes
1
reply
842
views
How to extract beta coefficients from edgeR output
rnaseq
beta
coefficient
r
edger
updated 2.5 years ago by
Gordon Smyth
★ 7.0k • written 2.5 years ago by
RNAseqer
▴ 260
2
votes
1
reply
577
views
EdgeR exclude 0 count subjects for each gene
count
edgeR
R
updated 2.5 years ago by
Gordon Smyth
★ 7.0k • written 2.5 years ago by
RNAseqer
▴ 260
0
votes
0
replies
470
views
How do you convert vcf file to a genotype file useable by eigenstrat
conversion
vcf
format
eigenstrat
2.5 years ago by
RNAseqer
▴ 260
0
votes
0
replies
562
views
accessing the r-peer docker container.
docker
peer
r
2.5 years ago by
RNAseqer
▴ 260
0
votes
1
reply
604
views
Analysis of a SNPs moderating effect on disease
effect
SNP
moderating
updated 2.5 years ago by
colindaven
6.4k • written 2.6 years ago by
RNAseqer
▴ 260
5
votes
2
replies
915
views
Most well regarded piRNA detection pipeline/program
expression
piRNA
differential
smallRNAseq
detection
2.6 years ago by
RNAseqer
▴ 260
0
votes
0
replies
444
views
how to identiify real isomers in mirge3.0's output files.
isomirs
mirge3.0
2.6 years ago by
RNAseqer
▴ 260
0
votes
0
replies
864
views
REditools2 (HPC-reditools) de-novo editing prediction from RNAseq?
editing
reditools2
prediction
RNAseq
2.7 years ago by
RNAseqer
▴ 260
0
votes
3
replies
856
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
ATpoint
82k • written 2.8 years ago by
RNAseqer
▴ 260
0
votes
0
replies
469
views
Can you get individual sample counts from Spar (Small RNA-seq portal for analysis of sequencing experiments)
Differential
RNAseq
SPAR
Expression
2.9 years ago by
RNAseqer
▴ 260
0
votes
0
replies
504
views
getting residuals from dream
dream
limma
residuals
3.0 years ago by
RNAseqer
▴ 260
0
votes
0
replies
509
views
limma dream giving error message 'subscript out of bounds'
error
Dream
R
3.1 years ago by
RNAseqer
▴ 260
0
votes
0
replies
801
views
alternative package for littlesMCAR() or mcar_test()
littlesMCAR
MCAR
missingdata
3.1 years ago by
RNAseqer
▴ 260
5
votes
2
replies
832
views
Heirarchal regression for model comparison, RNA-seq
R
RNA-seq
heirarchalregression
updated 3.1 years ago by
ATpoint
82k • written 3.1 years ago by
RNAseqer
▴ 260
1
vote
5
replies
1.4k
views
chi squared assesment of gene expression and batch effect
RNA-Seq
r
chi squared
3.1 years ago by
RNAseqer
▴ 260
0
votes
1
reply
801
views
model matrix error message 'unequal columns/rows' when using a conditional variable
rna-seq
categorical variables
edger
updated 3.1 years ago by
Gordon Smyth
★ 7.0k • written 3.1 years ago by
RNAseqer
▴ 260
0
votes
1
reply
608
views
Nesting a covariate for differential expression design
RNA-Seq
nested
covariates
updated 3.1 years ago by
Biostar
20 • written 3.2 years ago by
RNAseqer
▴ 260
1
vote
1
reply
663
views
voomWithDreamWeights() has missing "NA" wheights for last samples
voomWithDreamWeights
dream
variaincePartition
3.1 years ago by
RNAseqer
▴ 260
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
alserg
▴ 920 • written 3.7 years ago by
RNAseqer
▴ 260
9
votes
4
replies
4.8k
views
A question regarding log2 transformation in EdgeR
EdgeR
log2
differentail expression analysis
updated 3.2 years ago by
Gordon Smyth
★ 7.0k • written 3.2 years ago by
RNAseqer
▴ 260
0
votes
0
replies
578
views
package for ICC plots from a matrix?
ICC
plots
R
3.2 years ago by
RNAseqer
▴ 260
2
votes
4
replies
761
views
Is miarma-Seq being maintained?
miarma-Seq
miRNA
RNA-Seq
3.4 years ago by
RNAseqer
▴ 260
0
votes
0
replies
559
views
best practices/ pipeline for miRNA sequencing QC
RNA-Seq
miRNA-seq
QC
3.4 years ago by
RNAseqer
▴ 260
0
votes
1
reply
1.0k
views
Is there a good reference matrix for miRNA array deconvolution?
miRNA
microarray
deconvolution
updated 3.7 years ago by
xinyiy027
• 0 • written 4.0 years ago by
RNAseqer
▴ 260
0
votes
1
reply
638
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
▴ 260
3
votes
2
replies
2.0k
views
affy Transcriptome Analysis Console (TAC), export expression matrix?
affy
TAC
expression matrix
4.0 years ago by
RNAseqer
▴ 260
1
vote
2
replies
717
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
Kevin Blighe
87k • written 4.1 years ago by
RNAseqer
▴ 260
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
swbarnes2
14k • written 4.2 years ago by
RNAseqer
▴ 260
4
votes
4
replies
1.5k
views
A good place to get immune cell deconvolution reference datasets?
deconvolution
reference datasets
updated 4.2 years ago by
jared.andrews07
★ 16k • written 4.2 years ago by
RNAseqer
▴ 260
3
votes
3
replies
1.6k
views
Correlating WGCNA modules to Diseased/Not-Diseased Trait
WGCNA
Modules
Traits
updated 4.6 years ago by
andres.firrincieli
3.6k • written 4.6 years ago by
RNAseqer
▴ 260
0
votes
1
reply
981
views
extracting a subset of probes from an expression object
subset
probes
microarray
exprs
updated 4.7 years ago by
Biostar
20 • written 4.9 years ago by
RNAseqer
▴ 260
1
vote
1
reply
5.1k
views
how to adjust for continuous covariates in limma?
limma
continuous covariates
DE
updated 4.8 years ago by
i.sudbery
19k • written 4.8 years ago by
RNAseqer
▴ 260
0
votes
0
replies
571
views
summarized probes with expresso. how do i get transcript IDs?
affy
expresso
transcript ID
4.8 years ago by
RNAseqer
▴ 260
0
votes
0
replies
877
views
is there an function to summarize miRNA array probes but do nothing else?
summarise probes
affy
miRNA
4.9 years ago by
RNAseqer
▴ 260
2
votes
5
replies
2.2k
views
changing feature names (row names) for expressionset object?
expressionset
limma
rownames
4.9 years ago by
RNAseqer
▴ 260
0
votes
0
replies
886
views
whats is the best normalization technique for miRNA microarray data?
normalization
miRNA
microarray
4.9 years ago by
RNAseqer
▴ 260
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
zx8754
11k • written 5.0 years ago by
RNAseqer
▴ 260
0
votes
0
replies
1.6k
views
making limma design matrix with covariates, a strange labelling issue?
limma
design matrix
labels
columns
5.0 years ago by
RNAseqer
▴ 260
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