Showing : Ballgown • reset
5
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14
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7.4k
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DESeq2 vs Ballgown results
ballgown deseq2
6.1 years ago CE ▴ 20
2
votes
8
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5.7k
views
StringTie + Ballgown: handling biological replicates
ballgown stringtie
updated 7.1 years ago by • 0 • written 8.1 years ago by ▴ 10
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
1
vote
7
replies
3.5k
views
How fold change is calculated in Ballgown?
ballgown
7.3 years ago Ir • 0
0
votes
7
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2.5k
views
Handling both technical and biological replicates in Ballgown
ballgown biologicalreplicates technical replicates stringtie
updated 6.4 years ago by ▴ 210 • written 7.1 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
1
vote
7
replies
1.8k
views
Ballgown object construction error
ballgown scan error package
6.9 years ago • updated 6.8 years ago spaque57 • 0
1
vote
5
replies
2.4k
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Error in stattest function
R rnaseq Ballgown
updated 2.9 years ago by • 0 • written 6.2 years ago by • 0
3
votes
5
replies
6.5k
views
Ballgown up and down regulated genes
ballgown differential expression
updated 7.0 years ago by • 0 • written 8.3 years ago by ▴ 10
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 7.5 years ago by • 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 7.1 years ago by • 0
0
votes
4
replies
359
views
Ballgown error in scan for c.tab files
ballgown RNASeq
11 weeks ago candacenewcome • 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
4
replies
1.7k
views
error reading ballgown object
R ballgown
6.2 years ago l.j.leach • 0
0
votes
3
replies
1.5k
views
Ballgown differential expression by exon problem
ballgown
5.6 years ago new_user • 0
0
votes
3
replies
1.9k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.0 years ago by 65k • written 6.0 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
3
votes
3
replies
1.8k
views
Specifying a Default Model in Ballgown
ballgown
updated 8.8 years ago by ▴ 210 • written 8.8 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
3
replies
1.4k
views
StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 22 months ago by ★ 3.9k • written 3.7 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
1
vote
3
replies
1.9k
views
limma regularization on Ballgown
ballgown limma
updated 6.8 years ago by ▴ 210 • written 6.9 years ago by ▴ 10
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
0
votes
2
replies
927
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
396
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
9 months ago Bushra • 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
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
2.2k
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
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
2
replies
978
views
RNA-Seq differential analysis with ballgown, getting more significantly deferentially expressed genes than significantly deferentially expressed tra…
ballgown
updated 5.9 years ago by 65k • written 5.9 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
2
votes
2
replies
1.5k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 5.2 years ago by 50k • written 5.2 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 5.2 years ago by ▴ 210 • written 5.2 years ago by • 0
1
vote
2
replies
863
views
Regularization of ballgown object on Limma
limma ballgown RNA-seq
4.2 years ago komuracom16 • 0
1
vote
1
reply
1.3k
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
1
reply
2.8k
views
Ballgown Error in file(file, "rt") : invalid 'description' argument
rna-seq ballgown
updated 6.6 years ago by ▴ 210 • written 6.6 years ago by • 0
0
votes
1
reply
1.9k
views
Ballgown with replicates and the adjustvars option
ballgown rnaseq differential gene expression
updated 6.4 years ago by ▴ 210 • written 6.7 years ago by • 0
0
votes
1
reply
893
views
ballgown time course design and command confirmation
ballgown stattest multiple time points
6.0 years ago yadongxue • 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
855
views
Ballgown for differential expressed genes
ballgown
5.9 years ago marasodi • 0
0
votes
1
reply
942
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
0
votes
1
reply
974
views
Error loading data, pheno_data names in 1st column do not match ballgown/sample dir names.
ballgown
5.8 years ago harris • 0
1
vote
1
reply
763
views
ballgown bamfiles vector
ballgown
5.7 years ago • updated 5.6 years ago jac1318 • 0
0
votes
1
reply
769
views
Ballgown Plotmeans problem
ballgown
5.6 years ago new_user • 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
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
0
votes
1
reply
771
views
Understanding the output from Ballgown for DE
changes ballgown
5.5 years ago amy16 • 0
0
votes
1
reply
2.1k
views
Can not install packages
ballgown genefilter RskittleBrewer
updated 5.4 years ago by ★ 6.5k • written 5.4 years ago by • 0
0
votes
1
reply
967
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
50 results • Page 1 of 1
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Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts by Michael Love 41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
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A: Docker container with bioconductor and devtools
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