Showing : Ballgown • reset
0
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4
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1.1k
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Ballgown error in scan for c.tab files
ballgown RNASeq
24 months ago candacenewcome • 0
1
vote
2
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967
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DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
2.5 years ago Bushra • 0
0
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1
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1.5k
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is.null(pData) | class(pData) == "data.frame" is not TRUE
ballgown
updated 4.4 years ago by 16k • written 4.4 years ago by • 0
1
vote
5
replies
3.3k
views
Error in stattest function
R rnaseq Ballgown
updated 4.7 years ago by • 0 • written 8.0 years ago by • 0
0
votes
1
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1.4k
views
Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 5.3 years ago by ★ 1.1k • written 5.3 years ago by • 0
0
votes
0
replies
2.1k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
5.3 years ago ra711 • 0
0
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1
reply
1.7k
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 5.4 years ago by ▴ 210 • written 5.4 years ago by • 0
0
votes
3
replies
2.4k
views
StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 3.6 years ago by ★ 4.0k • written 5.5 years ago by • 0
1
vote
2
replies
1.4k
views
Regularization of ballgown object on Limma
limma ballgown RNA-seq
6.0 years ago komuracom16 • 0
0
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0
replies
1.2k
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Is the ballgownrsem function still supported?
ballgown rsem iranges
6.1 years ago YH • 0
0
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0
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1.0k
views
ballgown -- how is statistical test performed
ballgown rna-seq
6.4 years ago michael • 0
0
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0
replies
981
views
ballgown: how to test for DE for my experimental setup
ballgown rna-seq
6.4 years ago michael • 0
0
votes
0
replies
2.4k
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
6.8 years ago fatimarasool135 • 0
1
vote
2
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1.7k
views
Ballgown Error .null(pData) | class(pData) == "data.frame" are not all TRUE
software error ballgown
updated 7.0 years ago by ▴ 210 • written 7.0 years ago by • 0
2
votes
2
replies
2.2k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 7.0 years ago by 53k • written 7.0 years ago by • 0
0
votes
0
replies
1.5k
views
Error while loading the data structrure in the ballgown tool
ballgown rnaseq differential gene expression new tuxedo pipleine
7.2 years ago Mithil Gaikwad • 0
0
votes
1
reply
2.6k
views
Can not install packages
ballgown genefilter RskittleBrewer
updated 7.2 years ago by ★ 6.6k • written 7.2 years ago by • 0
0
votes
0
replies
1.1k
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r ballgown
7.2 years ago viv333chavan • 0
0
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1
reply
1.1k
views
Understanding the output from Ballgown for DE
changes ballgown
7.3 years ago amy16 • 0
0
votes
0
replies
1.2k
views
R script to fix the error in dataframe when using ballgown for differentially expression analysis
r ballgown code error
7.3 years ago amy16 • 0
0
votes
3
replies
2.2k
views
Ballgown differential expression by exon problem
ballgown
7.4 years ago • updated 7.3 years ago new_user • 0
0
votes
1
reply
2.3k
views
Issue using ballgown
software error ballgown genomeinfodbdata genomeinfodb
updated 7.3 years ago by 68k • written 7.4 years ago by • 0
0
votes
2
replies
1.4k
views
Including batch effects in the differential expression of gene analysis
ballgown new tuxedo pipleine
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
1
vote
1
reply
1.1k
views
ballgown bamfiles vector
ballgown
7.4 years ago jac1318 • 0
0
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1
reply
1.1k
views
Ballgown Plotmeans problem
ballgown
7.4 years ago new_user • 0
0
votes
0
replies
1.3k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
7.5 years ago kicheol.kim • 0
1
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0
replies
2.5k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
7.6 years ago • updated 7.5 years ago kicheol.kim • 0
0
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1
reply
1.3k
views
Error loading data, pheno_data names in 1st column do not match ballgown/sample dir names.
ballgown
7.5 years ago harris • 0
1
vote
0
replies
1.6k
views
covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
7.6 years ago justinjj ▴ 10
0
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0
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1.4k
views
pair wise ballgown
ballgown differential expression
7.6 years ago zoe.ward • 0
0
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1
reply
1.3k
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
0
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1
reply
1.3k
views
Ballgown for differential expressed genes
ballgown
7.6 years ago marasodi • 0
0
votes
2
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1.4k
views
Ballgown for differential expressed genes
ballgown
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
1
vote
2
replies
2.2k
views
RNA-Seq differential analysis with ballgown, getting more significantly deferentially expressed genes than significantly deferentially expressed tra…
ballgown
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
0
votes
0
replies
2.4k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2 stringtie ballgown RNAseq
7.9 years ago • updated 7.7 years ago Nancy ▴ 10
0
votes
0
replies
1.9k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
7.7 years ago vharshavardhanan • 0
0
votes
0
replies
985
views
pairwise comparison with ballgown
ballgown
7.8 years ago behnam.derakhshani • 0
0
votes
0
replies
1.2k
views
Model problem using ballgown
ballgown linear models
7.8 years ago Yong Li ▴ 50
0
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1
reply
1.4k
views
ballgown time course design and command confirmation
ballgown stattest multiple time points
7.8 years ago yadongxue • 0
0
votes
3
replies
2.4k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
0
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0
replies
993
views
Ballgown data read error
ballgown software error
7.8 years ago amy16 • 0
5
votes
14
replies
9.2k
views
DESeq2 vs Ballgown results
ballgown deseq2
7.9 years ago • updated 7.8 years ago CE ▴ 20
1
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1
reply
1.9k
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 7.9 years ago by 68k • written 7.9 years ago by ▴ 80
2
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4
replies
2.2k
views
error reading ballgown object
R ballgown
8.0 years ago l.j.leach • 0
0
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0
replies
1.2k
views
Subset functionin R
R ballgown rnaseq
8.0 years ago amy16 • 0
0
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0
replies
1.1k
views
Accessing the assembly data-output
R rnaseq ballgown
8.0 years ago amy16 • 0
0
votes
3
replies
2.3k
views
error in filtering genes with rowVars(gexpr(bg_chrX)) >1
genefilter ballgown
updated 8.0 years ago by • 0 • written 8.5 years ago by • 0
1
vote
3
replies
3.4k
views
Multiple pairwise comparisons in ballgown
ballgown
updated 8.0 years ago by ▴ 210 • written 8.0 years ago by ▴ 10
1
vote
2
replies
2.0k
views
Error in reading ballgown object
R ballgown
updated 8.0 years ago by ▴ 210 • written 8.0 years ago by • 0
0
votes
7
replies
3.4k
views
Handling both technical and biological replicates in Ballgown
ballgown biologicalreplicates technical replicates stringtie
updated 8.2 years ago by ▴ 210 • written 8.9 years ago by • 0
75 results • Page 1 of 2
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Replies
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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