Showing : Ballgown • reset
2
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8
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5.7k
views
StringTie + Ballgown: handling biological replicates
ballgown stringtie
updated 7.2 years ago by • 0 • written 8.2 years ago by ▴ 10
0
votes
7
replies
2.5k
views
Handling both technical and biological replicates in Ballgown
ballgown biologicalreplicates technical replicates stringtie
updated 6.4 years ago by ▴ 210 • written 7.2 years ago by • 0
1
vote
7
replies
1.8k
views
Ballgown object construction error
ballgown scan error package
6.9 years ago spaque57 • 0
3
votes
3
replies
1.8k
views
Specifying a Default Model in Ballgown
ballgown
updated 8.9 years ago by ▴ 210 • written 8.9 years ago by • 0
2
votes
5
replies
4.0k
views
processing data with 2 rep or one replicate by ballgown
ballgown differential gene expression
updated 7.5 years ago by ▴ 210 • written 7.6 years ago by • 0
3
votes
5
replies
6.6k
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Ballgown up and down regulated genes
ballgown differential expression
updated 7.0 years ago by • 0 • written 8.3 years ago by ▴ 10
1
vote
5
replies
2.4k
views
Error in stattest function
R rnaseq Ballgown
updated 2.9 years ago by • 0 • written 6.3 years ago by • 0
0
votes
3
replies
1.8k
views
error in filtering genes with rowVars(gexpr(bg_chrX)) >1
genefilter ballgown
updated 6.3 years ago by • 0 • written 6.7 years ago by • 0
5
votes
14
replies
7.4k
views
DESeq2 vs Ballgown results
ballgown deseq2
6.1 years ago CE ▴ 20
1
vote
7
replies
3.5k
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How fold change is calculated in Ballgown?
ballgown
7.3 years ago Ir • 0
2
votes
4
replies
1.7k
views
error reading ballgown object
R ballgown
6.3 years ago l.j.leach • 0
0
votes
4
replies
1.8k
views
Results with very few genes with qval <0.05
ballgown
updated 7.1 years ago by • 0 • written 7.2 years ago by • 0
2
votes
7
replies
3.1k
views
ballgown custom models
ballgown linear model model matrix custom model
8.1 years ago • updated 8.0 years ago sbcn ▴ 80
0
votes
2
replies
936
views
Including batch effects in the differential expression of gene analysis
ballgown new tuxedo pipleine
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
0
votes
2
replies
1.4k
views
IRanges error loading rsem data into ballgown
ballgown
updated 7.2 years ago by ▴ 650 • written 7.2 years ago by • 0
1
vote
2
replies
420
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
9 months ago Bushra • 0
0
votes
4
replies
1.8k
views
Ballgown from StringTie results transcripts which are not expressed in both conditions as Differentially expressed ones
ballgown stringtie
updated 7.8 years ago by ▴ 650 • written 7.8 years ago by • 0
2
votes
2
replies
1.0k
views
Ballgown Custom Model Question
ballgown rnaseq
updated 7.7 years ago by ▴ 650 • written 7.7 years ago by • 0
1
vote
3
replies
1.4k
views
Interaction term analysis using ballgown
ballgown stringtie voom limma differential gene expression rnaseq
updated 7.6 years ago by ▴ 210 • written 7.6 years ago by ▴ 10
0
votes
2
replies
1.8k
views
I'm worried that I can't use "ballgown" well
ballgown rnaseq
updated 7.5 years ago by 65k • written 7.5 years ago by • 0
0
votes
2
replies
2.3k
views
HISAT-StringTie-Ballgown, order of biological replicates in script design
ballgown rna-seq
updated 7.3 years ago by ▴ 210 • written 7.3 years ago by • 0
0
votes
8
replies
3.7k
views
The common error with ballgown has not been solved!
ballgown software error
updated 7.2 years ago by ▴ 650 • written 7.2 years ago by ▴ 10
0
votes
1
reply
1.7k
views
P value <0.05 and Q values~ 1
ballgown
updated 6.9 years ago by ▴ 650 • written 6.9 years ago by • 0
1
vote
3
replies
1.9k
views
limma regularization on Ballgown
ballgown limma
updated 6.9 years ago by ▴ 210 • written 6.9 years ago by ▴ 10
0
votes
1
reply
1.9k
views
Ballgown with replicates and the adjustvars option
ballgown rnaseq differential gene expression
updated 6.5 years ago by ▴ 210 • written 6.7 years ago by • 0
0
votes
1
reply
2.8k
views
Ballgown Error in file(file, "rt") : invalid 'description' argument
rna-seq ballgown
updated 6.7 years ago by ▴ 210 • written 6.7 years ago by • 0
1
vote
1
reply
1.4k
views
RNA-seq for DGE
stringtie illumina hisat2 ballgown
updated 6.5 years ago by ▴ 120 • written 6.5 years ago by • 0
1
vote
3
replies
2.6k
views
Multiple pairwise comparisons in ballgown
ballgown
updated 6.3 years ago by ▴ 210 • written 6.3 years ago by ▴ 10
1
vote
2
replies
1.5k
views
Error in reading ballgown object
R ballgown
updated 6.3 years ago by ▴ 210 • written 6.3 years ago by • 0
1
vote
1
reply
1.4k
views
What is the exact formula for the calculation of Fold Change (FC), p-val and q-val in Ballgown stattest?
ballgown stattest fold change
updated 6.2 years ago by 65k • written 6.2 years ago by ▴ 80
0
votes
3
replies
1.9k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.1 years ago by 65k • written 6.1 years ago by • 0
1
vote
2
replies
1000
views
RNA-Seq differential analysis with ballgown, getting more significantly deferentially expressed genes than significantly deferentially expressed tra…
ballgown
updated 6.0 years ago by 65k • written 6.0 years ago by • 0
0
votes
2
replies
1.0k
views
Ballgown for differential expressed genes
ballgown
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
1
reply
951
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
1
vote
1
reply
776
views
ballgown bamfiles vector
ballgown
5.7 years ago jac1318 • 0
0
votes
1
reply
1.8k
views
Issue using ballgown
software error ballgown genomeinfodbdata genomeinfodb
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
0
votes
3
replies
2.0k
views
Error in ball gown command
rnaseq ballgown differential gene expression
updated 7.4 years ago by ▴ 650 • written 7.4 years ago by ▴ 10
0
votes
1
reply
2.1k
views
Can not install packages
ballgown genefilter RskittleBrewer
updated 5.5 years ago by ★ 6.5k • written 5.5 years ago by • 0
2
votes
2
replies
1.6k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 5.3 years ago by 50k • written 5.3 years ago by • 0
1
vote
2
replies
1.1k
views
Ballgown Error .null(pData) | class(pData) == "data.frame" are not all TRUE
software error ballgown
updated 5.3 years ago by ▴ 210 • written 5.3 years ago by • 0
1
vote
2
replies
882
views
Regularization of ballgown object on Limma
limma ballgown RNA-seq
4.3 years ago komuracom16 • 0
0
votes
3
replies
1.4k
views
StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 22 months ago by ★ 3.9k • written 3.8 years ago by • 0
0
votes
1
reply
1.2k
views
Error loading sample and control data using Ballgown due to different i_id in i_data.ctab
ballgown i_data.ctab differential gene expression
updated 3.6 years ago by ▴ 210 • written 3.7 years ago by • 0
0
votes
1
reply
981
views
Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 3.5 years ago by ★ 1.0k • written 3.5 years ago by • 0
0
votes
4
replies
396
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
0
votes
1
reply
866
views
Ballgown for differential expressed genes
ballgown
5.9 years ago marasodi • 0
0
votes
0
replies
1.3k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
3.6 years ago ra711 • 0
0
votes
0
replies
989
views
pair wise ballgown
ballgown differential expression
5.9 years ago zoe.ward • 0
1
vote
0
replies
1.3k
views
covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
5.8 years ago justinjj ▴ 10
1
vote
0
replies
2.0k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
5.8 years ago kicheol.kim • 0
50 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
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