Showing : RNAseq • reset
6
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5
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2.4k
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Calculating standard deviation for a few genes using RNAseq data
edger RNAseq
updated 5.1 years ago by ★ 13k • written 5.1 years ago by • 0
3
votes
6
replies
1.5k
views
EdgeR design matrix with 3 factors
edgeR glm RNAseq
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
3
votes
6
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2.6k
views
deseq2 + filtering low counts with noiseq function
deseq2 noiseq lowcounts rnaseq
updated 3.7 years ago by 43k • written 5.1 years ago by ▴ 10
1
vote
7
replies
1.5k
views
How to get multi-factor Deseq LRT test log P values for a particular condition
Deseq2 LRT Factors RNAseq
5.1 years ago aishu.jp ▴ 30
5
votes
8
replies
2.2k
views
Sort decreasing only numeric columns (more than one) in a dataframe with character and numeric column
sort R RNAseq character numeric
updated 5.1 years ago by ▴ 220 • written 5.1 years ago by ▴ 10
0
votes
2
replies
4.2k
views
CPM function in EDGER
edger cpm rnaseq
5.1 years ago francesca3 • 0
0
votes
1
reply
1.0k
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 30
1
vote
1
reply
1.0k
views
Can I add raw counts for duplicated genes?
DESeq2 RNAseq
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
8
votes
11
replies
1.9k
views
Is there any model in EdgeR that is close to nested ANOVA?
edger rnaseq
updated 5.2 years ago by 53k • written 5.2 years ago by ▴ 10
2
votes
2
replies
1.3k
views
edgeR batch effect correction for unevenly distributed groups
rnaseq edgeR batch effect
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
0
votes
3
replies
2.1k
views
StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 3.3 years ago by ★ 4.0k • written 5.2 years ago by • 0
0
votes
0
replies
808
views
EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeq normalization GC length RNASeq
5.2 years ago abf ▴ 30
1
vote
5
replies
3.5k
views
Spearman correlation for RNA SEQ data
deseq2 rnaseq statistic
updated 5.3 years ago by ★ 3.4k • written 5.3 years ago by • 0
0
votes
8
replies
1.2k
views
Deseq2 weird values for Log2FC and pvalue.
deseq2 rnaseq r
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
3
replies
823
views
DESeq2 Design Model and Results Function Set-Up - How to know if using the interaction term is appropriate?
deseq2 rnaseq
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
1
reply
1.0k
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
0
votes
9
replies
2.4k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
5.3 years ago camillab. ▴ 10
1
vote
6
replies
13k
views
Change fontsize/remove name of annotation ComplexHeatmap package
r rnaseq complexHeatmap annotation
updated 5.3 years ago by ▴ 290 • written 5.3 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 5.3 years ago by 53k • written 5.3 years ago by • 0
0
votes
0
replies
1.6k
views
Job: Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
software engineer RNASeq proteomics Job visualisation
5.3 years ago Laurent Gatto 1.6k
2
votes
7
replies
2.9k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 5.3 years ago by 53k • written 5.3 years ago by • 0
4
votes
14
replies
2.3k
views
Application of quantro to RNASeq: I do not get the same results as are in the quantro paper supplement
quantro RNASeq
updated 5.4 years ago by ▴ 80 • written 5.4 years ago by ▴ 30
2
votes
1
reply
1.7k
views
Cross-species analysis and normalization with DESeq2
normalization deseq2 across species rnaseq
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
1
vote
8
replies
2.8k
views
[Outlier Gene removal] - One sample with outlier counts for some genes
RNAseq DESeq2 outlier counts DE analysis
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
1
vote
7
replies
3.0k
views
tximport from RSEM expected counts: is it possible to import from a table rather than a file?
tximport limma rnaseq
updated 4.5 years ago by • 0 • written 5.4 years ago by ▴ 60
2
votes
2
replies
2.7k
views
How to Analyse Datasets from GEO
geo rnaseq deseq2 tpm
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by ▴ 10
5
votes
3
replies
2.1k
views
Multi-level experiments in Limma
limma rnaseq r
updated 5.4 years ago by 53k • written 5.4 years ago by ▴ 10
2
votes
4
replies
2.9k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
2
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4
replies
2.1k
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria GO KEEG RNAseq
5.4 years ago liz.marjory • 0
0
votes
8
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2.0k
views
Weird MA-plot (DESeq2)
deseq2 RNAseq
5.5 years ago jgarces • 0
5
votes
7
replies
3.5k
views
Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 5.5 years ago by 53k • written 5.5 years ago by ▴ 60
3
votes
5
replies
2.1k
views
Different numbers of DE genes using edgeR and DESEQ2
edger deseq2 rnaseq de
updated 5.5 years ago by 53k • written 5.5 years ago by ▴ 60
6
votes
6
replies
3.0k
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go DE edger rnaseq glmTreat
updated 5.5 years ago by 53k • written 5.5 years ago by ▴ 60
3
votes
1
reply
628
views
Reverse calculate counts using DESeq2 normalised values
deseq2 rnaseq
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
1
vote
1
reply
757
views
Differential Expression by Chromosome using edgeR
edgeR chromosome RNAseq
updated 5.5 years ago by ★ 1.4k • written 5.5 years ago by • 0
0
votes
2
replies
984
views
estimating variability in absence of replicates for edgeR
edgeR RNAseq voom variability estimator
updated 5.5 years ago by 53k • written 5.5 years ago by • 0
4
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2
replies
942
views
Multiple testing across both contrasts and genes using the "nestedF" method
limma rnaseq
5.6 years ago fl ▴ 20
0
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8
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1.4k
views
DESeq2 notice about GLM convergence
deseq2 RNASeq
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
6
replies
2.0k
views
Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
2
votes
8
replies
1.5k
views
DESEQ2 design with unequal matching and replicates?
deseq2 RNASeq
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
1
reply
1.4k
views
What does an asymmetrical MA plot indicate and how do I know if it means I've made an error?
deseq2 plotMA rnaseq community analysis asymmetry
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
2
votes
4
replies
1.6k
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
7
replies
1.7k
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
5.6 years ago rafaelsolersanblas ▴ 50
1
vote
2
replies
1.7k
views
For loop for DESeq2
loop deseq2 rnaseq
updated 3.3 years ago by • 0 • written 5.6 years ago by ▴ 10
1
vote
2
replies
1.9k
views
How to create better separation in PCA plot
PCA plot RNAseq
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by ▴ 10
0
votes
0
replies
1.2k
views
RNAseq/miRNAseq normalization for calculating gene correlations, survival analysis, and exploratory graphing
limma edger voom rnaseq mirnaseq
5.7 years ago atakanekiz ▴ 30
1
vote
0
replies
1.4k
views
News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
5.7 years ago Laurent Gatto 1.6k
3
votes
5
replies
1.7k
views
Emirical Bayesian shrinkage for dispertion/LFC estimation
rnaseq deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 10
0
votes
2
replies
1.1k
views
DESeq2 Complex Model
deseq2 rnaseq
updated 5.7 years ago by ★ 13k • written 5.7 years ago by ▴ 10
0
votes
2
replies
2.3k
views
How should I normalize my RNAseq data from Polysome profiling
deseq2 bioconductor RNAseq normalization Polysome_profiling
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1,409 results • Page 9 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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