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<prev • 338 results • page 1 of 12 • next >
2
votes
1
answer
202
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5 follow
1
answer
How to normalized TPM with TMM method?
tpm rna-seq edger tmm written 6 weeks ago by xiaoguang • 10 • updated 3 days ago by Gordon Smyth • 950
3
votes
0
answers
77
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5 follow
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Tutorial: Normalization of BigWig files using TMM from edgeR
deeptools tutorial bigwig edger tmm written 4 days ago by ATpoint ♦ 21k
3
votes
1
answer
119
views
1
answer
analysis of multiple batches and multiple treatment conditions in scRNA-seq
scrna-seq deseq2 combat limma edger written 16 days ago by Bogdan • 850 • updated 15 days ago by sofiagreen72211 • 30
2
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1
answer
811
views
1
answer
edgeR : How to test differential exon usage on case/control study across all time points when accounting for the within subject variability?
model time-course model.matrix edger lrt written 2.0 years ago by sarin.heikki.v • 10 • updated 20 days ago by h.mon ♦ 26k
1
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0
answers
98
views
0
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DEG tool for just 2 pair end data
deseq2 limma rna-seq edger written 20 days ago by sabaghianamir70 • 0 • updated 20 days ago by RamRS ♦ 23k
14
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2
answers
274
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6 follow
2
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edgeR DGElist Error: Negative counts not allowed.
edger written 27 days ago by ma23 • 20 • updated 24 days ago by Gordon Smyth • 950
2
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0
answers
1.1k
views
0
answers
Why DESeq2 filter and remove genes with high count?
gene R deseq2 edger written 2.9 years ago by star • 190 • updated 24 days ago by Biostar ♦♦ 20
0
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0
answers
60
views
0
answers
Model Matrix Interacting model
next-gen rna-seq edger model/design matrix written 28 days ago by akh22 • 30
1
vote
1
answer
137
views
1
answer
comparing kallisto rsem , makind sd plot and corelation table /graph
rsem deseq2 kallisto edger rnaseqcomp written 4 weeks ago by yusuf • 10 • updated 4 weeks ago by WouterDeCoster ♦ 40k
18
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2
answers
169
views
7 follow
2
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Doing differential gene expression without knowing sample classes
deseq2 rna-seq edger written 4 weeks ago by F • 3.4k
1
vote
1
answer
159
views
1
answer
Is calcuNormFactors necessary in the calculation of RPKM?
rpkm rna-seq edger written 6 weeks ago by wangdp123 • 160 • updated 6 weeks ago by ATpoint ♦ 21k
1
vote
1
answer
952
views
1
answer
diffSplice: Error in exon.genes[o, , drop = FALSE] : incorrect number of dimensions
exon diffsplice edger voom written 2.0 years ago by sarin.heikki.v • 10 • updated 6 weeks ago by Gordon Smyth • 950
0
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0
answers
184
views
0
answers
model matrix for longitudinal pairwise data: linear regression or linear mixed model?
rnaseq model matrix deseq2 edger limma written 7 weeks ago by agm123 • 0
1
vote
1
answer
147
views
1
answer
Filtering proteomics matrix before diff. exp.
deseq2 limma edger written 8 weeks ago by rpraveenkumarbio • 10 • updated 8 weeks ago by JC ♦ 8.2k
2
votes
1
answer
205
views
1
answer
which data is more suitable for Heatmap?
next-gen rna-seq edger heatmap written 9 weeks ago by star • 190 • updated 9 weeks ago by ATpoint ♦ 21k
2
votes
1
answer
163
views
5 follow
1
answer
edgeR and design matrix with triplicates
R edger rna-seq written 9 weeks ago by elb • 160 • updated 9 weeks ago by ATpoint ♦ 21k
3
votes
1
answer
167
views
1
answer
edgeR FDR always 1
fdr differentialexpression edger mirna written 9 weeks ago by AngAdd • 0 • updated 9 weeks ago by swbarnes2 ♦ 6.1k
1
vote
0
answers
181
views
0
answers
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
R ruvseq ruv glm edger written 10 weeks ago by garbuzov • 10
8
votes
2
answers
337
views
2
answers
How to perform multiple comparisons using edgeR?
rna-seq edger written 11 weeks ago by silas008 • 100
2
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0
answers
238
views
0
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Up/Down regulated genes list in EdgeR
diffrential gene expression rna-seq edger written 10 weeks ago by ali.hakimzadeh • 0
2
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1
answer
181
views
1
answer
Can use log(CPM) of Pairwise comparison as expression level?
rna-seq edger gene-expression written 10 weeks ago by star • 190
0
votes
1
answer
120
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1
answer
trouble abundance_estimates_to_matrix.pl (trinity2.4.0)
trinity rna-seq edger written 11 weeks ago by 1353288408 • 0 • updated 11 weeks ago by h.mon ♦ 26k
2
votes
0
answers
191
views
0
answers
filter data by normalization
R tcga rna-seq edger written 4 months ago by leandrogarcia20504 • 0 • updated 11 weeks ago by Biostar ♦♦ 20
5
votes
2
answers
240
views
2
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what to do when differential analysis heatmap looks like this?
R differentialanalysis rna-seq edger heatmap written 12 weeks ago by newbie • 70 • updated 12 weeks ago by eric.audemard • 0
0
votes
1
answer
171
views
1
answer
Abundance Counting for Non-Model Organism for edgeR
rna-seq abundance edger written 12 weeks ago by sdbaney • 0 • updated 12 weeks ago by ATpoint ♦ 21k
5
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2
answers
339
views
2
answers
How to do scaling in ComplexHeatmap
R chip-seq edger complexheatmap written 3 months ago by sophialovechan • 40 • updated 12 weeks ago by zx8754 ♦ 7.9k
0
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0
answers
123
views
0
answers
What type of GTF file should I use for miRNAseq analysis?
rna-seq edger mirna written 12 weeks ago by silas008 • 100
1
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0
answers
175
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0
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Differential gene expression using edgeR and using a generalised linear model (GLM)
R rna-seq edger written 12 weeks ago by ali.hakimzadeh • 0
2
votes
1
answer
178
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1
answer
edgeR analysis outputs FDR equals 1
fdr rna-seq edger written 3 months ago by silas008 • 100 • updated 3 months ago by swbarnes2 ♦ 6.1k
3
votes
0
answers
313
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0
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DESeq2 (or EdgeR) Exploratory Analysis with no Replicates
deseq2 edger rna-seq written 3 months ago by gabriel.jabud • 20
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