0
votes
3
replies
1.4k
views
Design matrix for cohort with samples outside "block"
limma voom sva
6.5 years ago kentfung ▴ 20
0
votes
1
reply
637
views
Question about design formulas in DESeq2 (4 genotypes, 2 batches, 2 cell states)
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
1
reply
1.3k
views
BiocCheck gives 'Error in readLines(file, skipNul = TRUE) : cannot open the connection'
BiocCheck
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
3
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6
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2.1k
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Is mm10.p6 available as BSgenome?
BSgenome.Mmusculus.UCSC.mm10
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 160
0
votes
11
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2.2k
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tx2gene for xenopus LAEVIS
deseq2
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
5
votes
13
replies
4.3k
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DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
2
replies
1.2k
views
Support for import of custom matrix data in the ddCt R package
ddCt import analysis R qRTPCR
updated 6.5 years ago by ▴ 120 • written 6.5 years ago by ▴ 10
2
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3
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Accounting for Gene Set Overlaps in Goana and Kegga Results
limma pathway
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ★ 1.6k
2
votes
1
reply
1.5k
views
biomaRt fails to retrieve GO description for some particular gene
biomart go r bioconductor symbol
6.5 years ago foehn ▴ 100
0
votes
1
reply
1.8k
views
timing when to use collapseReplicates in DESeq2
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
1
reply
1.3k
views
samples.txt?how to generate
deseq2
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
votes
0
replies
1.9k
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Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
6.6 years ago • updated 6.5 years ago Julie Zhu ★ 4.3k
2
votes
4
replies
2.0k
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DESeq2--compare two log2-transformed fold changes in paired and multi factor sample
deseq2
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 10
0
votes
0
replies
1.1k
views
Sample grouping (phenoData) and visualization in R package- HtqPCR
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6.5 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
457
views
how raw data is processed after estimation of mean-variation relation?
normalization deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
2
replies
1.1k
views
Reads with ambiguous annotation
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 60
0
votes
3
replies
1.7k
views
Help Generating Heat-maps between samples using WGCNA
WGCNA
6.5 years ago kgopotso.phakwago • 0
2
votes
2
replies
1.6k
views
What to do when a bug is found in a BioConductor package (Glimma)
glimma software error
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 10
0
votes
1
reply
1.0k
views
GUIDEseq outputDir error
GUIDEseq
updated 6.5 years ago by ★ 4.3k • written 6.5 years ago by ▴ 10
12
votes
9
replies
5.0k
views
Limma residuals matrix
limma
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 20
2
votes
4
replies
1.1k
views
Is magrittr "%>%" acceptable in bioc packages?
R bioconductor
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
2
votes
1
reply
2.3k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
0
votes
1
reply
1.7k
views
conda install of diffHic
diffHic conda
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
0
votes
7
replies
1.8k
views
How to change the size of yaxis in motifstack
motifstack plotMotifLogoStack
6.5 years ago saadmurtazakhan ▴ 10
0
votes
1
reply
402
views
Identifying unique DEG and synergistically affected genes in a combination treatment (DESeq2)
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
2
replies
3.0k
views
How can I delete specific rows (using gene name) from a DESeq2 dataset (or even just a counts file.
deseq2
updated 6.5 years ago by ★ 13k • written 6.5 years ago by • 0
0
votes
0
replies
837
views
fsva function does not work without newdat argument
sva
6.5 years ago jakob.wirbel • 0
0
votes
5
replies
1.8k
views
EnsemblGene ID conversion
deseq2 annotation Tutorial
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
0
votes
3
replies
1.7k
views
How to apply a linear mixed model onto an RNA-Seq data?
limma linear mixed model voom rna-seq
6.5 years ago Assa Yeroslaviz ★ 1.5k
0
votes
0
replies
1.0k
views
plotROC collapsing ROC curves into single line
anaquin plotroc
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
0
votes
4
replies
988
views
The meaning of interaction terms in design matrix in edgeR User's Guide on page 38
edger
updated 6.5 years ago by 53k • written 6.5 years ago by • 0
4
votes
6
replies
1.9k
views
Feature selection across batches in simpleSingleCell when spike-ins are not available.
simpleSingleCell
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
1
vote
1
reply
1.1k
views
Feature selection across batches in simpleSingleCell "Correcting batch effects" vignette
simpleSingleCell
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
0
votes
0
replies
1.1k
views
Different versions of r/affy combination may lead to differences in rma normalization results
microarray affy rma normalization affy package
6.5 years ago yshuang • 0
0
votes
0
replies
1.2k
views
Error on labeledHeatmap() function - WGCNA 1.68
WGCNA R
6.5 years ago feltrin88 • 0
0
votes
1
reply
618
views
about DESeq2 analysis on time series data
deseq2
6.5 years ago Cindy • 0
0
votes
3
replies
1.5k
views
GUIDEseq plus/minus strand inputs
GUIDEseq
updated 6.5 years ago by ★ 4.3k • written 6.5 years ago by ▴ 10
1
vote
6
replies
2.4k
views
how to download bigwig from recount2?
recount
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
0
votes
1
reply
984
views
GUIDEseq bam input
GUIDEseq bam
updated 6.5 years ago by ★ 4.3k • written 6.5 years ago by ▴ 10
1
vote
2
replies
1.1k
views
Using WGCNA for purposes other than RNA-SEQ/Microarray
WGCNA R
updated 6.5 years ago by ★ 3.0k • written 6.5 years ago by • 0
1
vote
2
replies
3.0k
views
CDF not found
Affy microarray
updated 6.5 years ago by ★ 4.1k • written 6.5 years ago by ▴ 10
0
votes
1
reply
472
views
Sai Nikhith Cholleti
edger deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
1
reply
1.3k
views
DESeq2 - Comparing RNA-Seq and Ribo-Seq
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
4
replies
1.7k
views
DropletUtils' emptyDrops() fails with non-integer counts
DropletUtils
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
0
votes
1
reply
1.6k
views
org.Hs.eg.db can not be downloaded
org.Hs.eg.db
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
0
votes
4
replies
1.3k
views
DEseq2 analysis time-series data under two conditions
deseq2
6.5 years ago Cindy • 0
0
votes
0
replies
902
views
Estimating survival function with left truncation?
Icens Survival Left-truncation Interval-Censored
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
0
votes
0
replies
1.2k
views
The correct specification of the model matrix to ComBat
ComBat sva
6.5 years ago Sam ▴ 10
0
votes
3
replies
2.8k
views
Can't install Genesis
Genesis Installation
updated 6.5 years ago by ★ 6.6k • written 6.5 years ago by ▴ 10
22
votes
12
replies
32k
views
New function lfcShrink() in DESeq2
deseq2
updated 6.5 years ago by • 0 • written 8.8 years ago by 43k
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