Showing : RNA-Seq • reset
3
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Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
4.5 years ago • updated 4.4 years ago Antonio M. • 0
1
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2
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1.6k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 4.5 years ago by 53k • written 4.5 years ago by ▴ 20
1
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7
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2.0k
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how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
4.5 years ago decppced • 0
1
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3
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1.2k
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Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
0
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0
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1.2k
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Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
4.7 years ago wrzl • 0
3
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9
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3.2k
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summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
4.8 years ago Pufall, Miles A ▴ 30
0
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1
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1.4k
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Limma/Voom Normalized Counts
limma RNA-seq
updated 4.8 years ago by 53k • written 4.8 years ago by • 0
0
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2
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2.4k
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RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 4.9 years ago by 53k • written 4.9 years ago by ▴ 70
0
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2
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1.7k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 2.4 years ago by • 0 • written 4.9 years ago by • 0
3
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6
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4.1k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 4.6 years ago by 43k • written 4.9 years ago by ▴ 10
0
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3
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2.3k
views
GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 4.9 years ago by ★ 3.4k • written 5.0 years ago by ▴ 70
0
votes
3
replies
1.6k
views
Weird set of samples in plant gene atlas study that appear over-corrected after DESeq2 normalization
RNA-Seq DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
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0
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1.7k
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule microarray RNA-seq WGCNA
5.0 years ago • updated 4.9 years ago modarzi ▴ 10
0
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0
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1.4k
views
Job: Bioinformatics Developer / Computational Biologist
bioinformatics rna-seq shiny apps R algorithm development Job
5.0 years ago mmartin ▴ 20
0
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0
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1.1k
views
circRNAprofiler - miRNA binding sites
circRNA RNA-seq circRNAprofiler
5.0 years ago Terra • 0
0
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0
replies
1.9k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
5.0 years ago ra711 • 0
3
votes
3
replies
1.5k
views
Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 10
0
votes
3
replies
1.8k
views
Pathway analysis of bacterial RNA-seq data
annotation rna-seq pathway analysis
5.0 years ago microPhD • 0
5
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6
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2.3k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 20
3
votes
1
reply
1.2k
views
How do you create a targets dataframe in edgeR?
edgeR RNA-SEQ
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
1
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1
reply
1.6k
views
Having issues mapping gene Ids during ReportingTools::publish() from Bioconductor.
ReportingTools RNA-Seq RMarkdown
updated 5.1 years ago by 68k • written 5.1 years ago by ▴ 20
1
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4
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2.5k
views
Issues with DESeq2 LRT for time-course experiment
rna-seq R DESeq2 LRT
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by ▴ 10
0
votes
1
reply
1.3k
views
dupRadar: low % of duplicates for 150bp PE RNAseq
dupRadar 150bp RNA-seq
updated 5.1 years ago by ▴ 80 • written 5.1 years ago by • 0
1
vote
4
replies
2.5k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 10
0
votes
0
replies
1.7k
views
Job: Scientist 1, Bioinformatics (Research | Berkeley, CA | Full Time)
Bioinformatics drug-discovery RNA-seq CRISPR Job
5.1 years ago yzhang • 0
0
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0
replies
1.3k
views
Job: Postdoctoral Fellow in Sars-CoV-2 genomics and transcriptomics @ Paul-Ehrlich-Institute, Germany
rna-seq phylogenetics protein modelling single-cell sequencing Job
5.2 years ago liam.childs • 0
3
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2
replies
6.6k
views
DESeq2 design formula with multiple factors
deseq2 RNA-Seq
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 10
0
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2
replies
3.8k
views
cmdscale() error: NA values not allowed in 'd', ask for help.
cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq
updated 5.2 years ago by ▴ 980 • written 5.3 years ago by ▴ 10
7
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6
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1.5k
views
Odd DESeq2 results - high significance in genes with too many zeros
deseq2 rna-seq
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
1
vote
2
replies
1.2k
views
EdgeR blocking factor - missing paired sample
EdgeR edgeR RNA-seq differential expression analysis blocking factors
updated 5.3 years ago by 53k • written 5.3 years ago by ▴ 60
0
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2
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2.2k
views
DESeq2 doubts about transformations + nbinomWaldtest warning
rna-seq deseq2 warnings nbinomWaldTest transformation
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
1
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0
replies
1.3k
views
Pathview : why are some genes not colored?
pathview rna-seq
5.3 years ago okna0215 ▴ 10
1
vote
0
replies
1.5k
views
Job: Bioinformatics Data Analyst
R RNA-seq job Job
5.3 years ago António Miguel de Jesus Domingues ▴ 510
1
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4
replies
2.4k
views
How to compare a single RNA-Seq sample with microarray samples?
voom rna-seq microarray
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 10
4
votes
8
replies
3.3k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 2.7 years ago by 68k • written 5.3 years ago by ▴ 30
0
votes
2
replies
3.5k
views
Normalisation of rlog and VSD transformation
deseq2 rna-seq R
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by ▴ 10
3
votes
8
replies
4.5k
views
Normalisation in DESeq2
deseq2 rna-seq
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by ▴ 10
1
vote
3
replies
2.6k
views
Pairwise comparison of multiple groups with different base
deseq2 rna-seq r
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
4
votes
6
replies
5.5k
views
linear mixed models using edgeR+limma
linear mixed model edger limma voom RNA-seq
updated 5.4 years ago by 53k • written 5.4 years ago by ▴ 10
1
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7
replies
3.7k
views
High padj in DESeq2
deseq2 RNA-seq microRNA
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by ▴ 10
2
votes
2
replies
2.2k
views
subsetting VST counts from one dataset
deseq2 rna-seq
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 60
0
votes
1
reply
788
views
Where to file data for RNA-seq workflow: gene-level exploratory analysis and differential expression?
rna-seq
updated 5.4 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
3
votes
4
replies
2.1k
views
Massive L2FC in DESeq2
deseq2 ashr rna-seq
5.4 years ago Alex • 0
1
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1
reply
2.1k
views
EDASeq gene length normalization
edaseq r rna-seq
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
0
votes
1
reply
748
views
Having issues generating manhattan plot in deseq2
deseq2 RNA-seq
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
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0
replies
1.1k
views
Export Results from BatchQC Shiny App
BatchQC RNA-seq R Shiny batch-effect
5.5 years ago manninm • 0
0
votes
5
replies
3.4k
views
Using raw pvalue instead of adjusted pvalue in Deseq 2
DESeq2 RNA-seq
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
2
votes
4
replies
3.0k
views
DESeq2 Error: package or namespace load failed for 'DESeq2'
RNA-Seq DESeq2
updated 5.5 years ago by ▴ 50 • written 5.5 years ago by ▴ 10
2
votes
1
reply
1.5k
views
batchelor batch correction correction runs into errors
batchelor batch-correction mnncorrect fastmnn rna-seq
updated 5.5 years ago by ★ 29k • written 6.1 years ago by ▴ 20
4
votes
3
replies
1.5k
views
Rsamtools summarizeOverlaps produces low counts
Rsamtools summarizeOverlaps RNA-seq
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 10
418 results • Page 2 of 9
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Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Answer: Help with defining groups by Gordon Smyth 53k
Defining sample groups is separate to reading in the DIA-NN data, because the sample conditions and covariates are not necessarily coded in…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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