Showing : Rnaseq • reset
2
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3
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2.0k
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Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 7.3 years ago by ▴ 980 • written 7.3 years ago by • 0
3
votes
5
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1.0k
views
DESeq2: possible to compare read counts at single nucleotide level ?
deseq2 rnaseq
updated 7.3 years ago by 53k • written 7.3 years ago by • 0
3
votes
8
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3.2k
views
EdgeR for differential analysis between two cell lines without replication
edger differential gene expression rnaseq
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 120
0
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2
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3.2k
views
What are the different strategies to filter out low count genes?
rnaseq deseq2 differential gene expression
updated 7.3 years ago by ★ 13k • written 7.3 years ago by ▴ 80
0
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1
reply
1.2k
views
Using tximport on RSEM abundance date
rnaseq rsem tximport
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
2
votes
3
replies
965
views
Run edgeR or Voom+LIMMA where groups are dynamically reassigned for each gene.
rnaseq limma edger
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 60
5
votes
9
replies
6.1k
views
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
deseq2 rnaseq
updated 7.3 years ago by ▴ 10 • written 10.5 years ago by ▴ 70
1
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5
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1.6k
views
Differential analysis based on selection of random samples
r differential gene expression deseq2 bioconductor rnaseq
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 60
1
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0
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1.6k
views
covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
7.3 years ago justinjj ▴ 10
2
votes
4
replies
8.0k
views
Understanding Contrasts when analyzing DESeq2 results
deseq2 extracting contrasts rnaseq interaction term
updated 7.3 years ago by ★ 1.4k • written 7.3 years ago by ▴ 10
0
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0
replies
1.0k
views
How to output list of genes which belong to specific GO(Gene Ontology)?
gene ontology rnaseq
7.3 years ago karagozeylul • 0
0
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0
replies
1.1k
views
ASPLI (RNAseq AS) R package error
rnaseq ASPLI
7.3 years ago dina.hesham139 • 0
0
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0
replies
1.1k
views
How to output list of genes which belong to specific GO(Gene Ontology)?
rnaseq gene ontology
7.3 years ago karagozeylul • 0
0
votes
2
replies
1.3k
views
Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq edgeR makecontrasts interactions
updated 7.3 years ago by ★ 29k • written 7.3 years ago by ▴ 90
3
votes
12
replies
5.9k
views
The calculation of regularized logarithm
rnaseq deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
0
votes
0
replies
1.4k
views
Job: Postdoctoral position, T follicular helper cell transcriptomics
single cell rnaseq T cells Tfh cells immunology Job
7.3 years ago michela.locci • 0
0
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0
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1.5k
views
Job: Post-doc in Prostate Cancer Research (Statistics / Computational Biology) at University of St Andrews (+PhD position also available)
cancer sequencing rnaseq methylation smallrna Job
7.3 years ago Andy Lynch ▴ 120
3
votes
7
replies
2.0k
views
Compare effect size of gene (lfcShrink or not)
deseq2 rnaseq
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
7
votes
15
replies
7.5k
views
Differentially expressed genes selection with FC and FDR cutoff
edgeR rnaseq r bioconductor
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 60
1
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2
replies
2.4k
views
very different DESeq2 results between two versions
deseq2 rnaseq
7.3 years ago sven.schenk ▴ 30
4
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4
replies
3.2k
views
Applying varianceStabilizingTransformation to log transformed RNA seq data from cBioPortal
variancestabilizingtransformation rnaseq cBioPortal deseq2
updated 7.3 years ago by ▴ 20 • written 7.3 years ago by • 0
0
votes
0
replies
1.6k
views
Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
7.4 years ago manuelmendoza • 0
2
votes
3
replies
1.8k
views
ASE using DESeq2
deseq2 deseq normalization allele specific expression rnaseq
updated 7.4 years ago by ★ 3.8k • written 7.4 years ago by • 0
1
vote
2
replies
3.5k
views
DESeq2 with CIBERSORT cell proportions?
deseq2 rnaseq
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
7
votes
6
replies
7.2k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 7.4 years ago by 53k • written 7.4 years ago by ▴ 60
4
votes
2
replies
8.5k
views
DESeq2 : normalized counts
rnaseq deseq2 normalized counts
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
7
votes
11
replies
6.2k
views
Comparing means of VST tranformed RNA-Seq counts in different groups of samples with boxplots
VST deseq2 boxplot rnaseq
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 90
1
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2
replies
743
views
Analysis guidance for data inclusion in deseq2 analysis: data subsets vs contrasts
deseq2 rnaseq
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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0
replies
1.1k
views
0 values in cuff_data file from cummeRbund
cummeRbund cuff_data rnaseq cuffset
7.4 years ago alexandra.holden.2015 • 0
5
votes
4
replies
3.4k
views
Why DESeq2 and edgeR give different results?
deseq2 rnaseq differential gene expression edger
updated 4.4 years ago by 53k • written 7.4 years ago by ▴ 120
2
votes
9
replies
1.8k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 7.4 years ago by ★ 29k • written 7.4 years ago by ▴ 20
0
votes
1
reply
934
views
Normalized Values of Multi Sample Count Matrix with DESeq2
rnaseq deseq2 normalization
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Warning message RSQLite::Id in CummeRbund
bioconductor rnaseq cummerbund
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
1
vote
19
replies
30k
views
Import bamfiles for RNAsequencing analysis
R rnaseq bam file
updated 7.4 years ago by 53k • written 7.5 years ago by ▴ 10
0
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0
replies
2.3k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2 stringtie ballgown RNAseq
7.7 years ago • updated 7.4 years ago Nancy ▴ 10
0
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0
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1.8k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
7.4 years ago vharshavardhanan • 0
3
votes
6
replies
5.8k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 7.4 years ago by 68k • written 7.4 years ago by ▴ 120
0
votes
1
reply
1.0k
views
DESeq2 design for time series data without "untreated"
deseq2 rnaseq multiple time points
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
votes
1
reply
951
views
RNAseq DESeq2 paired data design help
rnaseq design matrix deseq2
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
32
votes
16
replies
21k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 7.5 years ago by ▴ 20 • written 9.3 years ago by ▴ 200
5
votes
6
replies
1.4k
views
AveLogCPM of a library subset
edger rnaseq
updated 7.5 years ago by ★ 29k • written 7.5 years ago by ▴ 20
0
votes
0
replies
838
views
monocle estimateSizeFactors give Inf for all values
rnaseq
7.5 years ago jonessara770 ▴ 10
3
votes
5
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2.2k
views
EdgeR: Prior degrees of freedom effect on tag wise dispersion
R edgeR rnaseq rna-seq
updated 7.5 years ago by ★ 29k • written 7.5 years ago by ▴ 20
2
votes
4
replies
6.0k
views
WGCNA: intrepreting grey unassigned "module"?
WGCNA rnaseq gene expression co-expression network
updated 7.5 years ago by ★ 3.0k • written 7.5 years ago by ▴ 10
2
votes
4
replies
1.3k
views
Limma model for paired and pool together
limma design rnaseq
updated 7.5 years ago by ★ 7.9k • written 7.5 years ago by ▴ 370
2
votes
5
replies
2.2k
views
Accessing R 3.4.2 version on mac, to use 'rnaseqGene' package
rnaseq rnaseqgene R 3.4.2 Mac
updated 7.5 years ago by 4.2k • written 7.5 years ago by • 0
1
vote
10
replies
1.7k
views
Allele-specific expression with different gene lenghts
deseq2 allele-specific-expression rnaseq
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 10
0
votes
4
replies
4.4k
views
featureCounts taking 4-10 hours per BAM file?
featurecounts r rnaseq
7.5 years ago octopuslegs11 • 0
1
vote
5
replies
1.8k
views
Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
7.5 years ago David R ▴ 90
1,409 results • Page 13 of 29
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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