Showing : Ballgown • reset
0
votes
4
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445
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Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
1
vote
2
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433
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DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
10 months ago Bushra • 0
0
votes
1
reply
979
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is.null(pData) | class(pData) == "data.frame" is not TRUE
ballgown
updated 2.7 years ago by 16k • written 2.7 years ago by • 0
1
vote
5
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2.5k
views
Error in stattest function
R rnaseq Ballgown
updated 3.0 years ago by • 0 • written 6.3 years ago by • 0
0
votes
1
reply
989
views
Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 3.6 years ago by ★ 1.0k • written 3.6 years ago by • 0
0
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0
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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
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1
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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 3.7 years ago by ▴ 210 • written 3.7 years ago by • 0
0
votes
3
replies
1.5k
views
StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 23 months ago by ★ 3.9k • written 3.8 years ago by • 0
1
vote
2
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899
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Regularization of ballgown object on Limma
limma ballgown RNA-seq
4.3 years ago komuracom16 • 0
0
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0
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821
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
4.4 years ago YH • 0
0
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0
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664
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ballgown -- how is statistical test performed
ballgown rna-seq
4.7 years ago michael • 0
0
votes
0
replies
618
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
5.1 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 5.3 years ago by ▴ 210 • written 5.3 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
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
5.5 years ago Mithil Gaikwad • 0
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
0
votes
0
replies
834
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r ballgown
5.6 years ago viv333chavan • 0
0
votes
1
reply
789
views
Understanding the output from Ballgown for DE
changes ballgown
5.6 years ago amy16 • 0
0
votes
0
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790
views
R script to fix the error in dataframe when using ballgown for differentially expression analysis
r ballgown code error
5.6 years ago amy16 • 0
0
votes
3
replies
1.6k
views
Ballgown differential expression by exon problem
ballgown
5.7 years ago new_user • 0
0
votes
1
reply
1.8k
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
945
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
784
views
ballgown bamfiles vector
ballgown
5.7 years ago jac1318 • 0
0
votes
1
reply
786
views
Ballgown Plotmeans problem
ballgown
5.7 years ago new_user • 0
0
votes
0
replies
975
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
1
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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
5.9 years ago • updated 5.8 years ago kicheol.kim • 0
0
votes
1
reply
997
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
5.9 years ago justinjj ▴ 10
0
votes
0
replies
997
views
pair wise ballgown
ballgown differential expression
5.9 years ago zoe.ward • 0
0
votes
1
reply
959
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.9 years ago by 66k • written 5.9 years ago by • 0
0
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1
reply
877
views
Ballgown for differential expressed genes
ballgown
6.0 years ago marasodi • 0
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2
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1.0k
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Ballgown for differential expressed genes
ballgown
updated 6.0 years ago by 66k • written 6.0 years ago by • 0
1
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2
replies
1.0k
views
RNA-Seq differential analysis with ballgown, getting more significantly deferentially expressed genes than significantly deferentially expressed tra…
ballgown
updated 6.0 years ago by 66k • written 6.0 years ago by • 0
0
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0
replies
1.9k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2 stringtie ballgown RNAseq
6.3 years ago • updated 6.0 years ago Nancy ▴ 10
0
votes
0
replies
1.4k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.0 years ago vharshavardhanan • 0
0
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0
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723
views
pairwise comparison with ballgown
ballgown
6.1 years ago behnam.derakhshani • 0
0
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0
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841
views
Model problem using ballgown
ballgown linear models
6.1 years ago Yong Li ▴ 50
0
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1
reply
915
views
ballgown time course design and command confirmation
ballgown stattest multiple time points
6.1 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 6.1 years ago by 66k • written 6.1 years ago by • 0
0
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0
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740
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Ballgown data read error
ballgown software error
6.1 years ago amy16 • 0
5
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14
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7.5k
views
DESeq2 vs Ballgown results
ballgown deseq2
6.2 years ago CE ▴ 20
1
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1
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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 6.2 years ago by 66k • written 6.2 years ago by ▴ 80
2
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4
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1.7k
views
error reading ballgown object
R ballgown
6.3 years ago l.j.leach • 0
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0
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819
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Subset functionin R
R ballgown rnaseq
6.3 years ago amy16 • 0
0
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0
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833
views
Accessing the assembly data-output
R rnaseq ballgown
6.3 years ago amy16 • 0
0
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3
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1.8k
views
error in filtering genes with rowVars(gexpr(bg_chrX)) >1
genefilter ballgown
updated 6.3 years ago by • 0 • written 6.8 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 6.4 years ago by ▴ 10
1
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2
replies
1.5k
views
Error in reading ballgown object
R ballgown
updated 6.3 years ago by ▴ 210 • written 6.4 years ago by • 0
0
votes
7
replies
2.5k
views
Handling both technical and biological replicates in Ballgown
ballgown biologicalreplicates technical replicates stringtie
updated 6.5 years ago by ▴ 210 • written 7.2 years ago by • 0
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt by blackwidowzzz • 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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