Showing : Ballgown • reset
0
votes
4
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474
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Ballgown error in scan for c.tab files
ballgown RNASeq
4 months ago candacenewcome • 0
1
vote
2
replies
450
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
11 months ago Bushra • 0
0
votes
1
reply
999
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is.null(pData) | class(pData) == "data.frame" is not TRUE
ballgown
updated 2.8 years ago by 16k • written 2.8 years ago by • 0
1
vote
5
replies
2.5k
views
Error in stattest function
R rnaseq Ballgown
updated 3.0 years ago by • 0 • written 6.4 years ago by • 0
0
votes
1
reply
1.0k
views
Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 3.6 years ago by ★ 1.1k • written 3.6 years ago by • 0
0
votes
0
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1.4k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
3.7 years ago ra711 • 0
0
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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 3.8 years ago by ▴ 210 • written 3.8 years ago by • 0
0
votes
3
replies
1.5k
views
StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 24 months ago by ★ 3.9k • written 3.9 years ago by • 0
1
vote
2
replies
918
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Regularization of ballgown object on Limma
limma ballgown RNA-seq
4.4 years ago komuracom16 • 0
0
votes
0
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850
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Is the ballgownrsem function still supported?
ballgown rsem iranges
4.5 years ago YH • 0
0
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0
replies
670
views
ballgown -- how is statistical test performed
ballgown rna-seq
4.7 years ago michael • 0
0
votes
0
replies
627
views
ballgown: how to test for DE for my experimental setup
ballgown rna-seq
4.7 years ago michael • 0
0
votes
0
replies
1.8k
views
Error in contrasts<-(tmp, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels
software error ballgown rstudio R stattest
5.2 years ago fatimarasool135 • 0
1
vote
2
replies
1.1k
views
Ballgown Error .null(pData) | class(pData) == "data.frame" are not all TRUE
software error ballgown
updated 5.4 years ago by ▴ 210 • written 5.4 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 5.4 years ago by 51k • written 5.4 years ago by • 0
0
votes
0
replies
1.1k
views
Error while loading the data structrure in the ballgown tool
ballgown rnaseq differential gene expression new tuxedo pipleine
5.6 years ago Mithil Gaikwad • 0
0
votes
1
reply
2.1k
views
Can not install packages
ballgown genefilter RskittleBrewer
updated 5.6 years ago by ★ 6.5k • written 5.6 years ago by • 0
0
votes
0
replies
843
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r ballgown
5.6 years ago viv333chavan • 0
0
votes
1
reply
797
views
Understanding the output from Ballgown for DE
changes ballgown
5.7 years ago amy16 • 0
0
votes
0
replies
806
views
R script to fix the error in dataframe when using ballgown for differentially expression analysis
r ballgown code error
5.7 years ago amy16 • 0
0
votes
3
replies
1.6k
views
Ballgown differential expression by exon problem
ballgown
5.8 years ago • updated 5.7 years ago new_user • 0
0
votes
1
reply
1.9k
views
Issue using ballgown
software error ballgown genomeinfodbdata genomeinfodb
updated 5.7 years ago by 66k • written 5.7 years ago by • 0
0
votes
2
replies
954
views
Including batch effects in the differential expression of gene analysis
ballgown new tuxedo pipleine
updated 5.7 years ago by 66k • written 5.7 years ago by • 0
1
vote
1
reply
795
views
ballgown bamfiles vector
ballgown
5.8 years ago jac1318 • 0
0
votes
1
reply
797
views
Ballgown Plotmeans problem
ballgown
5.8 years ago new_user • 0
0
votes
0
replies
985
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
5.9 years ago kicheol.kim • 0
1
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0
replies
2.1k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
5.9 years ago kicheol.kim • 0
0
votes
1
reply
1.0k
views
Error loading data, pheno_data names in 1st column do not match ballgown/sample dir names.
ballgown
5.9 years ago harris • 0
1
vote
0
replies
1.3k
views
covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
6.0 years ago • updated 5.9 years ago justinjj ▴ 10
0
votes
0
replies
1.0k
views
pair wise ballgown
ballgown differential expression
6.0 years ago zoe.ward • 0
0
votes
1
reply
967
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 6.0 years ago by 66k • written 6.0 years ago by • 0
0
votes
1
reply
892
views
Ballgown for differential expressed genes
ballgown
6.0 years ago marasodi • 0
0
votes
2
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1.1k
views
Ballgown for differential expressed genes
ballgown
updated 6.0 years ago by 66k • written 6.0 years ago by • 0
1
vote
2
replies
1.0k
views
RNA-Seq differential analysis with ballgown, getting more significantly deferentially expressed genes than significantly deferentially expressed tra…
ballgown
updated 6.1 years ago by 66k • written 6.1 years ago by • 0
0
votes
0
replies
1.9k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2 stringtie ballgown RNAseq
6.3 years ago • updated 6.1 years ago Nancy ▴ 10
0
votes
0
replies
1.4k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.1 years ago vharshavardhanan • 0
0
votes
0
replies
728
views
pairwise comparison with ballgown
ballgown
6.2 years ago behnam.derakhshani • 0
0
votes
0
replies
848
views
Model problem using ballgown
ballgown linear models
6.2 years ago Yong Li ▴ 50
0
votes
1
reply
924
views
ballgown time course design and command confirmation
ballgown stattest multiple time points
6.2 years ago yadongxue • 0
0
votes
3
replies
1.9k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.2 years ago by 66k • written 6.2 years ago by • 0
0
votes
0
replies
750
views
Ballgown data read error
ballgown software error
6.2 years ago amy16 • 0
5
votes
14
replies
7.5k
views
DESeq2 vs Ballgown results
ballgown deseq2
6.3 years ago • updated 6.2 years ago CE ▴ 20
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 6.3 years ago by 66k • written 6.3 years ago by ▴ 80
2
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4
replies
1.7k
views
error reading ballgown object
R ballgown
6.4 years ago l.j.leach • 0
0
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0
replies
836
views
Subset functionin R
R ballgown rnaseq
6.4 years ago amy16 • 0
0
votes
0
replies
842
views
Accessing the assembly data-output
R rnaseq ballgown
6.4 years ago amy16 • 0
0
votes
3
replies
1.8k
views
error in filtering genes with rowVars(gexpr(bg_chrX)) >1
genefilter ballgown
updated 6.4 years ago by • 0 • written 6.9 years ago by • 0
1
vote
3
replies
2.7k
views
Multiple pairwise comparisons in ballgown
ballgown
updated 6.4 years ago by ▴ 210 • written 6.4 years ago by ▴ 10
1
vote
2
replies
1.6k
views
Error in reading ballgown object
R ballgown
updated 6.4 years ago by ▴ 210 • written 6.4 years ago by • 0
0
votes
7
replies
2.6k
views
Handling both technical and biological replicates in Ballgown
ballgown biologicalreplicates technical replicates stringtie
updated 6.5 years ago by ▴ 210 • written 7.3 years ago by • 0
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Comment: error loading collectTRI regulon by silvaesilva.da • 0
Fantastic. Thank you very much. Everything has been sorted out
Answer: DESeq2 returns results for group with just one replicate by James W. MacDonald 66k
There is no problem having only one replicate per group, so long as you have replicates for other groups. The degrees of freedom are based …
Answer: Limma model.matrix design with batch effect and different life stages proportion by Masongeorge • 0
Thanks for this post. i found it helpful for my own issue that was occurring on the backend of this page.
Comment: error loading collectTRI regulon by deeenes ▴ 50
I fixed the original, Ensembl HTTP 403 error only now, [see here][1]. If you've seen it gone earlier today, only shows that this error appe…
Answer: GESA with certain gene list returns no result with human genom, but many result by James W. MacDonald 66k
Ideally you would use something better than gene symbols for this. I realize that biologists like gene symbols, but they are really terribl…
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Comment: error loading collectTRI regulon
A: Scaling option in fastMNN
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
A: How to do a confounding variable adjustment without using the treatment informat
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