Showing : ballgown • reset
1
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DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
10 weeks ago Bushra • 0
0
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1
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738
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is.null(pData) | class(pData) == "data.frame" is not TRUE
ballgown
updated 2.1 years ago by 16k • written 2.1 years ago by • 0
1
vote
5
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2.1k
views
Error in stattest function
R rnaseq Ballgown
updated 2.3 years ago by • 0 • written 5.7 years ago by • 0
0
votes
1
reply
765
views
Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 2.9 years ago by ★ 1.0k • written 2.9 years ago by • 0
0
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0
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1.0k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
3.0 years ago ra711 • 0
0
votes
1
reply
940
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 3.0 years ago by ▴ 210 • written 3.0 years ago by • 0
0
votes
3
replies
1.1k
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StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 15 months ago by 3.8k • written 3.2 years ago by • 0
1
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2
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649
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Regularization of ballgown object on Limma
limma ballgown RNA-seq
3.7 years ago komuracom16 • 0
0
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0
replies
619
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Is the ballgownrsem function still supported?
ballgown rsem iranges
3.8 years ago YH • 0
0
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0
replies
500
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ballgown -- how is statistical test performed
ballgown rna-seq
4.0 years ago michael • 0
0
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0
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453
views
ballgown: how to test for DE for my experimental setup
ballgown rna-seq
4.0 years ago michael • 0
0
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0
replies
1.5k
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
4.5 years ago fatimarasool135 • 0
1
vote
2
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903
views
Ballgown Error .null(pData) | class(pData) == "data.frame" are not all TRUE
software error ballgown
updated 4.7 years ago by ▴ 210 • written 4.7 years ago by • 0
2
votes
2
replies
1.3k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 4.7 years ago by 48k • written 4.7 years ago by • 0
0
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0
replies
888
views
Error while loading the data structrure in the ballgown tool
ballgown rnaseq differential gene expression new tuxedo pipleine
4.9 years ago Mithil Gaikwad • 0
0
votes
1
reply
1.9k
views
Can not install packages
ballgown genefilter RskittleBrewer
updated 4.9 years ago by ★ 6.1k • written 4.9 years ago by • 0
0
votes
0
replies
684
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r ballgown
4.9 years ago viv333chavan • 0
0
votes
1
reply
659
views
Understanding the output from Ballgown for DE
changes ballgown
5.0 years ago amy16 • 0
0
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0
replies
622
views
R script to fix the error in dataframe when using ballgown for differentially expression analysis
r ballgown code error
5.0 years ago amy16 • 0
0
votes
3
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1.3k
views
Ballgown differential expression by exon problem
ballgown
5.1 years ago • updated 5.0 years ago new_user • 0
0
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1
reply
1.6k
views
Issue using ballgown
software error ballgown genomeinfodbdata genomeinfodb
updated 5.0 years ago by 63k • written 5.0 years ago by • 0
0
votes
2
replies
794
views
Including batch effects in the differential expression of gene analysis
ballgown new tuxedo pipleine
updated 5.0 years ago by 63k • written 5.0 years ago by • 0
1
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1
reply
630
views
ballgown bamfiles vector
ballgown
5.1 years ago jac1318 • 0
0
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1
reply
630
views
Ballgown Plotmeans problem
ballgown
5.1 years ago new_user • 0
0
votes
0
replies
783
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
5.2 years ago kicheol.kim • 0
1
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0
replies
1.9k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
5.2 years ago kicheol.kim • 0
0
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1
reply
844
views
Error loading data, pheno_data names in 1st column do not match ballgown/sample dir names.
ballgown
5.2 years ago harris • 0
1
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0
replies
1.0k
views
covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
5.2 years ago justinjj ▴ 10
0
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0
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812
views
pair wise ballgown
ballgown differential expression
5.3 years ago zoe.ward • 0
0
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1
reply
793
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.3 years ago by 63k • written 5.3 years ago by • 0
0
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1
reply
686
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Ballgown for differential expressed genes
ballgown
5.3 years ago marasodi • 0
0
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2
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865
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Ballgown for differential expressed genes
ballgown
updated 5.3 years ago by 63k • written 5.3 years ago by • 0
1
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2
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783
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RNA-Seq differential analysis with ballgown, getting more significantly deferentially expressed genes than significantly deferentially expressed tra…
ballgown
updated 5.4 years ago by 63k • written 5.4 years ago by • 0
0
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0
replies
1.6k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2 stringtie ballgown RNAseq
5.6 years ago • updated 5.4 years ago Nancy ▴ 10
0
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0
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1.1k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
5.4 years ago vharshavardhanan • 0
0
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0
replies
609
views
pairwise comparison with ballgown
ballgown
5.4 years ago behnam.derakhshani • 0
0
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0
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711
views
Model problem using ballgown
ballgown linear models
5.5 years ago Yong Li ▴ 50
0
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1
reply
750
views
ballgown time course design and command confirmation
ballgown stattest multiple time points
5.5 years ago yadongxue • 0
0
votes
3
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1.6k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 5.5 years ago by 63k • written 5.5 years ago by • 0
0
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0
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623
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Ballgown data read error
ballgown software error
5.5 years ago amy16 • 0
5
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14
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6.8k
views
DESeq2 vs Ballgown results
ballgown deseq2
5.5 years ago CE ▴ 20
1
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1
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1.1k
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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 5.6 years ago by 63k • written 5.6 years ago by ▴ 80
2
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4
replies
1.5k
views
error reading ballgown object
R ballgown
5.7 years ago l.j.leach • 0
0
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0
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663
views
Subset functionin R
R ballgown rnaseq
5.7 years ago amy16 • 0
0
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0
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684
views
Accessing the assembly data-output
R rnaseq ballgown
5.7 years ago amy16 • 0
0
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3
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1.6k
views
error in filtering genes with rowVars(gexpr(bg_chrX)) >1
genefilter ballgown
updated 5.7 years ago by • 0 • written 6.1 years ago by • 0
1
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3
replies
2.3k
views
Multiple pairwise comparisons in ballgown
ballgown
updated 5.7 years ago by ▴ 210 • written 5.7 years ago by ▴ 10
1
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2
replies
1.3k
views
Error in reading ballgown object
R ballgown
updated 5.7 years ago by ▴ 210 • written 5.7 years ago by • 0
0
votes
7
replies
2.3k
views
Handling both technical and biological replicates in Ballgown
ballgown biologicalreplicates technical replicates stringtie
updated 5.8 years ago by ▴ 210 • written 6.6 years ago by • 0
1
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1
reply
1.1k
views
RNA-seq for DGE
stringtie illumina hisat2 ballgown
updated 5.9 years ago by ▴ 120 • written 5.9 years ago by • 0
50 results • Page 1 of 1
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Answer: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by Mike Smith ★ 6.1k
I'll echo James' suggestion to use the GRCh37 mirror. Most mirrors only have a guaranteed lifetime of 5 years from Ensembl, although it se…
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by James W. MacDonald 63k
I should also point out that you can find this out by yourself by going to [ensembl][1], clicking on the Biomart link, and then scrolling t…
Answer: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by James W. MacDonald 63k
It's my understanding that the archived Biomart data are not complete, which is likely why you cannot get sequences. But you apparently jus…
Comment: ComBat_seq function in sva package does not return a matrix by Federico ▴ 10
Thanks for your help, problem solved :)
Answer: ComBat_seq function in sva package does not return a matrix by ATpoint ★ 3.4k
That happens if your `x` is a data.frame rather than a matrix. It is listed under the Q&A section in https://github.com/zhangyuqing/ComBat-…
Votes
ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
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