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
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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
views
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
419
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
9 months ago Bushra • 0
0
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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 6.1 years ago by 65k • written 6.1 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
950
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
881
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 3.6 years ago by • 0
0
votes
1
reply
980
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
392
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
0
votes
1
reply
865
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
988
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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Replies
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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