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hisat2-stringtie-ballgown pipeline gives high p-value and q-value for RNA-seq of Arabidopsis thaliana
ballgown arabidopsis stringtie rna-seq hisat2 written 19 months ago by tiancaigg • 10 • updated 12 days ago by 20482485 • 0
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100
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How to do differential gene expression analysis for samples from different tissue using Ballgown ?
ballgown tissue rna-seq written 23 days ago by sepand1818 • 0
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100
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HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
ballgown hisat2 stringtie isoform rna-seq written 24 days ago by ra711 • 0 • updated 24 days ago by genomax ♦ 91k
11
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1
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150
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1
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Gene vs Transcript Level DEG Analysis
ballgown rna-seq written 4 weeks ago by asumani • 60
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101
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What model is used by Ballgown?
ballgown rna-seq differential expression written 5 weeks ago by peter.brockport • 0
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133
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problem on ballgown
R ballgown rna-seq deg written 11 weeks ago by mo.ghasemi717 • 10
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1
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900
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5 follow
1
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ballgown has "." as Gene Names
assembly ballgown rna-seq written 21 months ago by Fawzi Yassine • 10 • updated 7 months ago by Sissi • 50
2
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1
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593
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1
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What is MSTRG?
stringtie mstrg ballgown rna-seq hisat2 written 9 months ago by arabi • 40
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How to make Heatmap about DEG?
ballgown rna-seq deg heatmap written 9 months ago by arabi • 40
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Stringtie output for DGE
stringtie ballgown written 2.9 years ago by amy16 • 40 • updated 10 months ago by Biostar ♦♦ 20
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465
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Invalid covariate name
R ballgown rna-seq written 11 months ago by mark.pekarsky • 20 • updated 11 months ago by Biostar ♦♦ 20
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6 follow
1
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Ballgown Error in file(file, "rt") : invalid 'description' argument
ballgown rna-seq written 3.2 years ago by vinayjrao • 180 • updated 14 months ago by wood • 0
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532
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ballgown and pData
ballgown rna-seq written 16 months ago by Morris_Chair • 200
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520
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Ballgown for visualization of gene expression
ballgown covariate written 19 months ago by dzo.ilic.i • 0 • updated 17 months ago by Biostar ♦♦ 20
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755
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Isoform level differential expression
stringtie ballgown rna-seq written 18 months ago by rnaseql • 0
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477
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How to add a specific column from related table
R bioconductor ballgown rna-seq written 20 months ago by Redse • 30
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2
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5 follow
2
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rowVars function, used in ballgown analysis not available for R 3.5.2, alternatives?
R ballgown rna-seq rowvars written 20 months ago by RNAseqer • 140 • updated 20 months ago by kristoffer.vittingseerup • 3.4k
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ballgown error: Error in file(file, "rt") : invalid 'description' argument Calls: ballgown -> read.table -> file
ballgown stringtie rna-seq written 20 months ago by RNAseqer • 140
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1
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Error while loading the data structrure in the ballgown tool
new tuxedo pipeline ballgown rna-seq written 23 months ago by swarajgaikwad15 • 20 • updated 23 months ago by lakhujanivijay ♦ 5.3k
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5 follow
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Ballgown finds few DE genes compared to DESeq
ballgown deseq2 rna-seq written 2.3 years ago by corend • 70 • updated 2.0 years ago by shenwei1376 • 0
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Problem in analysis of Ballgown output by R (why q value are same in result ? )
R ballgown differential expression (de) analysis written 2.1 years ago by amitunited0532 • 40 • updated 2.1 years ago by ATpoint ♦ 40k
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913
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Different results when visualizing tdf files in IGV and when doing the differential expression analysis with ballgown
assembly ballgown rna-seq igv written 2.1 years ago by iraia.munoa • 100 • updated 2.1 years ago by RamRS ♦ 30k
2
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1
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1.6k
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1
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FPKM matrix after stringtie using ballgown
stringtie ballgown fpkm rna-seq written 2.2 years ago by Vasu • 490 • updated 2.2 years ago by Adrian Pelin • 2.4k
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1
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838
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1
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Outputing gexpr() with gene_name (or gene symbol) instead of MSTRG.x gene_id
ballgown stringtie rna-seq gene_name written 2.2 years ago by ever_wudi • 10
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Stringtie prepDE.py Error line 32
stringtie deseq2 ballgown rna-seq prepde.py written 2.6 years ago by bryce.kirby • 0 • updated 2.4 years ago by Biostar ♦♦ 20
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Code for DEG analysis using Ballgown
ballgown stattest ngs rna-seq written 2.6 years ago by Arindam Ghosh • 310 • updated 2.5 years ago by lakhujanivijay ♦ 5.3k
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What measure should be used to calculate fold-change while using Ballgown to compare D.E genes between 2 conditions?
ballgown stringtie rna-seq hisat2 written 2.6 years ago by nancy • 90
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specification of linear model and log transformation in ballgown
package function R ballgown rna-seq written 2.8 years ago by amy16 • 40
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485
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ballgownrsem function usage details
ballgown tuxedo rna-seq dge written 2.8 years ago by amy16 • 40
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Error in reading ballgown object
R ballgown rna-seq written 2.8 years ago by amy16 • 40 • updated 2.8 years ago by WouterDeCoster ♦ 44k
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