Showing : Ballgown • reset
0
votes
4
replies
699
views
Ballgown error in scan for c.tab files
ballgown RNASeq
10 months ago • updated 9 months ago candacenewcome • 0
1
vote
2
replies
631
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
16 months ago Bushra • 0
0
votes
1
reply
1.2k
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is.null(pData) | class(pData) == "data.frame" is not TRUE
ballgown
updated 3.2 years ago by 16k • written 3.2 years ago by • 0
1
vote
5
replies
2.7k
views
Error in stattest function
R rnaseq Ballgown
updated 3.5 years ago by • 0 • written 6.8 years ago by • 0
0
votes
1
reply
1.1k
views
Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 4.1 years ago by ★ 1.1k • written 4.1 years ago by • 0
0
votes
0
replies
1.6k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
4.1 years ago ra711 • 0
0
votes
1
reply
1.4k
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 4.2 years ago by ▴ 210 • written 4.2 years ago by • 0
0
votes
3
replies
1.8k
views
StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 2.4 years ago by ★ 4.0k • written 4.3 years ago by • 0
1
vote
2
replies
1.1k
views
Regularization of ballgown object on Limma
limma ballgown RNA-seq
4.8 years ago komuracom16 • 0
0
votes
0
replies
990
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
4.9 years ago YH • 0
0
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0
replies
772
views
ballgown -- how is statistical test performed
ballgown rna-seq
5.2 years ago michael • 0
0
votes
0
replies
774
views
ballgown: how to test for DE for my experimental setup
ballgown rna-seq
5.2 years ago michael • 0
0
votes
0
replies
2.0k
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
5.6 years ago fatimarasool135 • 0
1
vote
2
replies
1.3k
views
Ballgown Error .null(pData) | class(pData) == "data.frame" are not all TRUE
software error ballgown
updated 5.8 years ago by ▴ 210 • written 5.8 years ago by • 0
2
votes
2
replies
1.8k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 5.8 years ago by 51k • written 5.8 years ago by • 0
0
votes
0
replies
1.3k
views
Error while loading the data structrure in the ballgown tool
ballgown rnaseq differential gene expression new tuxedo pipleine
6.0 years ago Mithil Gaikwad • 0
0
votes
1
reply
2.3k
views
Can not install packages
ballgown genefilter RskittleBrewer
updated 6.1 years ago by ★ 6.6k • written 6.1 years ago by • 0
0
votes
0
replies
947
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r ballgown
6.1 years ago viv333chavan • 0
0
votes
1
reply
894
views
Understanding the output from Ballgown for DE
changes ballgown
6.1 years ago amy16 • 0
0
votes
0
replies
926
views
R script to fix the error in dataframe when using ballgown for differentially expression analysis
r ballgown code error
6.1 years ago amy16 • 0
0
votes
3
replies
1.8k
views
Ballgown differential expression by exon problem
ballgown
6.2 years ago new_user • 0
0
votes
1
reply
2.0k
views
Issue using ballgown
software error ballgown genomeinfodbdata genomeinfodb
updated 6.2 years ago by 67k • written 6.2 years ago by • 0
0
votes
2
replies
1.1k
views
Including batch effects in the differential expression of gene analysis
ballgown new tuxedo pipleine
updated 6.2 years ago by 67k • written 6.2 years ago by • 0
1
vote
1
reply
900
views
ballgown bamfiles vector
ballgown
6.3 years ago • updated 6.2 years ago jac1318 • 0
0
votes
1
reply
902
views
Ballgown Plotmeans problem
ballgown
6.2 years ago new_user • 0
0
votes
0
replies
1.1k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.4 years ago kicheol.kim • 0
1
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0
replies
2.2k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.4 years ago kicheol.kim • 0
0
votes
1
reply
1.1k
views
Error loading data, pheno_data names in 1st column do not match ballgown/sample dir names.
ballgown
6.4 years ago harris • 0
1
vote
0
replies
1.4k
views
covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
6.4 years ago justinjj ▴ 10
0
votes
0
replies
1.2k
views
pair wise ballgown
ballgown differential expression
6.4 years ago zoe.ward • 0
0
votes
1
reply
1.1k
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 6.4 years ago by 67k • written 6.4 years ago by • 0
0
votes
1
reply
1.0k
views
Ballgown for differential expressed genes
ballgown
6.5 years ago marasodi • 0
0
votes
2
replies
1.2k
views
Ballgown for differential expressed genes
ballgown
updated 6.5 years ago by 67k • written 6.5 years ago by • 0
1
vote
2
replies
1.2k
views
RNA-Seq differential analysis with ballgown, getting more significantly deferentially expressed genes than significantly deferentially expressed tra…
ballgown
updated 6.5 years ago by 67k • written 6.5 years ago by • 0
0
votes
0
replies
2.1k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2 stringtie ballgown RNAseq
6.8 years ago • updated 6.6 years ago Nancy ▴ 10
0
votes
0
replies
1.5k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.6 years ago vharshavardhanan • 0
0
votes
0
replies
816
views
pairwise comparison with ballgown
ballgown
6.6 years ago behnam.derakhshani • 0
0
votes
0
replies
961
views
Model problem using ballgown
ballgown linear models
6.6 years ago Yong Li ▴ 50
0
votes
1
reply
1.1k
views
ballgown time course design and command confirmation
ballgown stattest multiple time points
6.6 years ago yadongxue • 0
0
votes
3
replies
2.1k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.6 years ago by 67k • written 6.6 years ago by • 0
0
votes
0
replies
819
views
Ballgown data read error
ballgown software error
6.6 years ago amy16 • 0
5
votes
14
replies
8.1k
views
DESeq2 vs Ballgown results
ballgown deseq2
6.7 years ago CE ▴ 20
1
vote
1
reply
1.5k
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 6.7 years ago by 67k • written 6.7 years ago by ▴ 80
2
votes
4
replies
1.9k
views
error reading ballgown object
R ballgown
6.8 years ago l.j.leach • 0
0
votes
0
replies
954
views
Subset functionin R
R ballgown rnaseq
6.8 years ago amy16 • 0
0
votes
0
replies
926
views
Accessing the assembly data-output
R rnaseq ballgown
6.8 years ago amy16 • 0
0
votes
3
replies
2.0k
views
error in filtering genes with rowVars(gexpr(bg_chrX)) >1
genefilter ballgown
updated 6.9 years ago by • 0 • written 7.3 years ago by • 0
1
vote
3
replies
2.9k
views
Multiple pairwise comparisons in ballgown
ballgown
updated 6.9 years ago by ▴ 210 • written 6.9 years ago by ▴ 10
1
vote
2
replies
1.8k
views
Error in reading ballgown object
R ballgown
updated 6.9 years ago by ▴ 210 • written 6.9 years ago by • 0
0
votes
7
replies
2.8k
views
Handling both technical and biological replicates in Ballgown
ballgown biologicalreplicates technical replicates stringtie
updated 7.0 years ago by ▴ 210 • written 7.7 years ago by • 0
50 results • Page 1 of 1
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Answer: Epic v2 Annotation CpG_maf source? by James W. MacDonald 67k
Those all come from dbSNP by way of UCSC. [See here][1], particularly lines 114 and onward. Here is no MAF for a CpG. The MAF is for the…
Comment: Deseq2 res Function by James W. MacDonald 67k
In addition to Mike's comment, do note that if you are generating a heatmap based on the set of significant genes, the direction of your co…
Answer: Struggle with the replicates of epic array data by James W. MacDonald 67k
You shouldn't be using beta values for a linear model that assumes a unimodal, untruncated distribution (beta values are strictly on (0-1) …
Comment: Identifying potentially associated gene set to drug response using GSVA by Robert Castelo ★ 3.4k
So, if I understand correctly, you derived GSVA scores from gene sets corresponding somehow to drugs in your RNA-seq data. Since GSVA score…
Answer: Deseq2 res Function by Michael Love 43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Votes
Appropriate use of the function treat of the limma package
Comment: Is it recommended to analyze different tissues together when using edgeR
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
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