1
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5
replies
1.9k
views
about DropletUtils and scRNA-seq
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updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 670
4
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9
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1.9k
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Statistical background for computing intial estimates for the means of negative binomially distributed gene counts in DESeq2
deseq2 design matrix
7.1 years ago nikosbosse • 0
0
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4
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5.3k
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Is lmFit() the fastest way to fit thousands of linear model in R and use what algorithm make it so fast ?
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updated 7.1 years ago by 68k • written 7.1 years ago by ▴ 30
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1.1k
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DESeq2 Design Formula
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updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
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3
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updated 7.1 years ago by 43k • written 7.1 years ago by • 0
1
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1
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1.0k
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deseq2: use blind=T or blind=F when find gene groups?
rlog transformation deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 20
0
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1
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1.5k
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What is the name of this probe?
affymetrix microarrays hta20transcriptcluster r select
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
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1
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News: List of Deprecated Package Bioc 3.9
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7.1 years ago shepherl 4.3k
2
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6
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2.4k
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Gviz color alignments by read strand
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updated 7.1 years ago by ▴ 750 • written 7.4 years ago by ▴ 40
0
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2
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32k
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DESeq2: interaction term
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7.1 years ago salamandra ▴ 20
4
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7
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6.5k
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removing rows from SingleCellExperiment container
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updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
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2
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1.6k
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Design matrix choice for time series experiment using limma
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updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
5
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14
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3.1k
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Odd P-value distribution in edgeR on RRBS data
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updated 7.1 years ago by 53k • written 7.1 years ago by • 0
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4
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1.1k
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RNA seq data
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updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
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0
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789
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Error while running ChAMP pipeline
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7.1 years ago sinha.puja ▴ 10
3
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1
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2.1k
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How to quantify or decide whether a covariate should be included in the linear model for differential expression analysis ?
limma edgeR deseq2
updated 7.1 years ago by 68k • written 7.1 years ago by ▴ 30
0
votes
4
replies
1.7k
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DESeq2 Ribosome Profiling Time-series: Significantly Different Results for Wald and LRT test
deseq2 ribosome profiling wald lrt
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 20
1
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3
replies
1.9k
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how to find expressed genes in RNAseq
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7.1 years ago melkile26 • 0
2
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9
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2.8k
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Gviz: decreasing tick resolution
gviz gviz-package
updated 7.1 years ago by ▴ 750 • written 7.1 years ago by • 0
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3
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1.5k
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Troubles with mzR and BiocInstaller
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7.1 years ago petr.hasler • 0
0
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2
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2.5k
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How can I compare the expression of two genes within the same sample?
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updated 7.1 years ago by ▴ 30 • written 7.1 years ago by • 0
0
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5
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1.8k
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connection to stringdb database server failed
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7.1 years ago julie • 0
1
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10
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2.4k
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questions regarding design that is similar to "Group-specific condition effects, individuals nested within groups"
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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5
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1.5k
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DESeq2 Parallel Computing Stall on Server
deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
0
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1
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1.3k
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HTqPCR: dealing with technical replicates (filterCategory) and inability to analyze datasets with filtered genes (limmaCtData).
limma htqpcr
updated 5.1 years ago by • 0 • written 7.1 years ago by • 0
6
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6
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DEseq2: Is vst/rlog transformation applied to raw counts or normalised counts?
deseq2 vst rlog transformation
updated 7.1 years ago by ★ 13k • written 7.1 years ago by ▴ 20
0
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1.3k
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DESeq2: plotMA looks wrong
deseq2
updated 7.1 years ago by ★ 13k • written 7.1 years ago by ▴ 10
2
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3
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tximport: kallisto .h5 files not recognized as such when they have a different name
tximport kallisto
updated 7.1 years ago by 53k • written 7.1 years ago by ▴ 40
4
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3
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1.7k
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Best way of creating a large RleMatrix
DelayedArray RleMatrix
updated 7.1 years ago by 16k • written 7.2 years ago by ▴ 180
0
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1
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1.2k
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Best Practices for Speeding Up/Optimizing EBIMage
ebimage
7.1 years ago grockmore • 0
0
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0
replies
833
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DiffBind - Difficulties construction appropriate consensus set
Diffbind
7.1 years ago Rob Buurstede • 0
0
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6
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2.5k
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how to achieve reproducibility with BiocParallel regardless of number of threads and OS (set.seed is disallowed)
BiocParallel
updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
7
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5
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2.4k
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scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 30
5
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1
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6.3k
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RNAseq analysis: what comes first, filtering or normalization
edger R rnaseq
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 30
0
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0
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955
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A problem about changeCtLayout in HTqPCR
htqpcr
7.1 years ago tropicalis • 0
0
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0
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1.2k
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ASpli AsDiscover error
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7.1 years ago abdul rawoof ▴ 60
1
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8
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2.3k
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DESeq2 model design for paired samples with multiple factors
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7.1 years ago swillis4 ▴ 10
0
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0
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697
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regionR randomizeRegions allow.overlaps option
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7.1 years ago crysis405 ▴ 10
0
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1
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1.5k
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Gene similarity by GOSemSim
gosemsim mgenesim
7.1 years ago athirak1986 • 0
0
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0
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1.7k
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vcf to venn diagram
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7.1 years ago mictadlo ▴ 10
3
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4
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2.7k
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Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 7.1 years ago by 53k • written 7.1 years ago by ▴ 30
1
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2
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2.9k
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Gviz: Setting Up Colour / Fill for AnnotationTrack (strand-dependent colour)
Gviz gviz-package GFF annotationtrack strand-dependent
updated 7.1 years ago by ▴ 750 • written 7.1 years ago by • 0
0
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0
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936
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Error in base::strsplit(x, ...) : non-character argument
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7.1 years ago catscampos • 0
3
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3
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3.7k
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Gene ID to Gene Name/Symbol in loom files
Scater LoomR SCopeloomR
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 20
0
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0
replies
1.6k
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
7.1 years ago bioinfouser2 ▴ 10
1
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1
reply
1.5k
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tximport of 3 tagged RNA-seq counts from Salmon for downstream analysis with DESeq2
tximport deseq2 rnaseq 3' tagged RNA
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 50
2
votes
3
replies
1.1k
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CalcNormFactors in Edge r
edger
updated 7.1 years ago by 53k • written 7.1 years ago by • 0
0
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0
replies
1.2k
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ggbio error when following tutorial, ideogram not highlighted, genetrack not working
ggbio ideogram autoplot
7.1 years ago gpwhiz ▴ 10
0
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1
reply
1.6k
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merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 50
1
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4
replies
2.0k
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Error in `rownames : Gviz plotTracks
gviz plottracks generegiontrack
7.1 years ago gpwhiz ▴ 10
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Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
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Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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