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GRangesList: wiered error
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8.2 years ago Fabian Grammes ▴ 20
2
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6
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Running DESeq2 with gene-dependent binary variable such as membership in pathway?
deseq2
updated 8.2 years ago by • 0 • written 8.2 years ago by • 0
0
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methyanalysis
8.2 years ago charleneee95 • 0
3
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5
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Found more than one class
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8.2 years ago Kamil Slowikowski ▴ 30
1
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7
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Cannot retrieve projects from TCGA using getGDCprojects function
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8.2 years ago jacorvar ▴ 40
0
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0
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Job: Postdoc in Computational Biology/Bioinformatics, IMB Mainz, Germany
job bioinformatics germany Job
8.2 years ago Mario Dejung • 0
1
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2
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Reading fastq file after narrowing sequences
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8.2 years ago ioannis.vardaxis ▴ 30
0
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2
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Differential expression between multiple groups
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8.2 years ago A ▴ 60
0
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Calling differential peaks from ATAC-seq data using DEseq2
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updated 8.2 years ago by ★ 5.2k • written 8.2 years ago by • 0
3
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Standardizing gene symbols
R
updated 8.2 years ago by 53k • written 8.2 years ago by ▴ 10
0
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0
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2.1k
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8.2 years ago ioannis.vardaxis ▴ 30
5
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6
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Analyzing data without replicates using DiffBind
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8.2 years ago Hesh ▴ 10
0
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5
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403 Forbidden During Install
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updated 8.2 years ago by ★ 6.8k • written 8.2 years ago by • 0
1
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1
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2.0k
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Trying to annotate microarray data and some probe set presents mismatch
annotation affymetrix microarrays
updated 8.2 years ago by 68k • written 8.2 years ago by • 0
1
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7
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deseq2 analysis with multiple factors and interaction terms
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updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
5
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edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
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updated 2.4 years ago by • 0 • written 8.2 years ago by ▴ 10
2
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2
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Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
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updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 60
1
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3
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2.1k
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Boxplot and Identification of DEG
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updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 20
1
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3
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Time-course group difference analysis with repeated individuals using limma-voom
limma
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ★ 1.1k
0
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0
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DEXSeq : Preprocessing within R for Forward-Reverse Library
DEXSeq
8.2 years ago ZheFrench ▴ 60
0
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2
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1.7k
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Unable to load sqlite file generated by Cuffdiff
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8.2 years ago handgabriel • 0
0
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1
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3.6k
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gseaplot() function of clusterProfiler went wrong
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8.2 years ago giuseppe0525 • 0
0
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1
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1.6k
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Solve overlapping gene labels in volcano plot when using textxy
R
8.2 years ago Nithisha ▴ 10
0
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0
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732
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Column name mismatch
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8.2 years ago zuolin.bai • 0
0
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1
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1.4k
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Running DESeq2 on top variable genes?
deseq2 variance genes
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
0
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3
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Design matrix for longitudinal discordant twin analysis with limma
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updated 8.2 years ago by ★ 29k • written 8.2 years ago by • 0
2
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derfinder mean Expressed Region cutoff
derfinder
updated 8.2 years ago by ★ 1.1k • written 8.2 years ago by ▴ 510
0
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0
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986
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Bugs in HTqPCR 1.30.0?
htqpcr
8.2 years ago h.roest • 0
0
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1
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2.0k
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DESeq2, lfcShrink, "Error in results(dds.shr, name = coefAlpha) : object 'coefAlpha' not found"
deseq2
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
0
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7
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2.0k
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Model matrix not full rank for condition-time experiment
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updated 8.2 years ago by 43k • written 8.2 years ago by • 0
0
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1
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1.8k
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Multi Anova in DESeq2
deseq2
updated 8.2 years ago by 43k • written 8.9 years ago by • 0
0
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1
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Error in checkFullRank(modelMatrix) : the model matrix is not full rank, ?
deseq2 filter genefilter
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
0
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4
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2.2k
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Time points and donors - errors with contrasts
deseq2 contrast
updated 8.2 years ago by 43k • written 8.5 years ago by • 0
0
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Normalize depth before calculating TPM
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8.2 years ago colore • 0
0
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3
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Error while processing BAM file with Picard FixMateInformation
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updated 8.2 years ago by • 0 • written 10.2 years ago by • 0
1
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2
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No differential expression with limmaCtData possible
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8.2 years ago h.roest • 0
0
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0
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invalid names for slots of class GOHyperGResult
gostats
8.2 years ago laianavarromartin ▴ 20
0
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0
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944
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interGeneCorrelation and voom
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8.2 years ago maltethodberg ▴ 180
0
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4
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How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo annotate
8.2 years ago llkxiaolan ▴ 10
5
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3
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Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapiens/Mus.musculus?
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updated 8.2 years ago by ★ 2.1k • written 8.2 years ago by ▴ 40
1
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2.0k
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Highlight ECs by KEGG module
pathview KEGG
updated 8.2 years ago by ★ 1.6k • written 8.2 years ago by • 0
0
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3
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How can I use DESeq2 for exploratory analysis after batch effect removal using RUVSeq?
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updated 8.2 years ago by 43k • written 8.2 years ago by • 0
2
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3
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2.2k
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GenomicRanges_RaggedExperiment Error in as background, class mcol no method or default for coercing logical to factor
genomicranges RaggedExperiment coercion logical factor
updated 8.2 years ago by 700 • written 8.2 years ago by • 0
0
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2
replies
24k
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Determining gene expression levels with DESeq2 in a design with no condition
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8.2 years ago robles.daniela • 0
1
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2
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2.4k
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DESeq2 for differential gene expression on GTEx dataset
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updated 8.2 years ago by 43k • written 8.2 years ago by • 0
2
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6
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GSEA using clusterProfiler
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8.2 years ago giuseppe0525 • 0
0
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2
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DiffBind dba.report inconsistent output when using filter parameters
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8.2 years ago konstantopoulos • 0
1
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1
reply
1.9k
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RNA-seq for DGE
stringtie illumina hisat2 ballgown
updated 8.2 years ago by ▴ 120 • written 8.2 years ago by • 0
1
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4
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cran check shows that genefilter is not available
genefilter
8.2 years ago jinkaixiu ▴ 10
0
votes
1
reply
1.6k
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Reference annotation file contains only transcript and CDS information, how to analyze the different expression of genes?
transcription hisat2
8.2 years ago zoukai3412085 • 0
46,726 results • Page 296 of 935
Recent ...
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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