Showing : Ballgown • reset
0
votes
4
replies
679
views
Ballgown error in scan for c.tab files
ballgown RNASeq
9 months ago candacenewcome • 0
1
vote
2
replies
618
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
16 months ago • updated 15 months ago Bushra • 0
0
votes
1
reply
1.1k
views
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 4.0 years ago by ★ 1.1k • written 4.1 years ago by • 0
0
votes
0
replies
1.5k
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
975
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
4.9 years ago YH • 0
0
votes
0
replies
759
views
ballgown -- how is statistical test performed
ballgown rna-seq
5.1 years ago michael • 0
0
votes
0
replies
766
views
ballgown: how to test for DE for my experimental setup
ballgown rna-seq
5.1 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 6.0 years ago by ★ 6.6k • written 6.0 years ago by • 0
0
votes
0
replies
932
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r ballgown
6.0 years ago viv333chavan • 0
0
votes
1
reply
882
views
Understanding the output from Ballgown for DE
changes ballgown
6.1 years ago amy16 • 0
0
votes
0
replies
917
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 • updated 6.1 years ago new_user • 0
0
votes
1
reply
2.0k
views
Issue using ballgown
software error ballgown genomeinfodbdata genomeinfodb
updated 6.1 years ago by 67k • written 6.1 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 6.1 years ago by 67k • written 6.1 years ago by • 0
1
vote
1
reply
891
views
ballgown bamfiles vector
ballgown
6.2 years ago jac1318 • 0
0
votes
1
reply
892
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
6.3 years ago kicheol.kim • 0
1
vote
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
6.3 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
6.3 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
1.1k
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
6.4 years ago marasodi • 0
0
votes
2
replies
1.1k
views
Ballgown for differential expressed genes
ballgown
updated 6.4 years ago by 67k • written 6.4 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
2.0k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2 stringtie ballgown RNAseq
6.7 years ago • updated 6.5 years ago Nancy ▴ 10
0
votes
0
replies
1.5k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.5 years ago vharshavardhanan • 0
0
votes
0
replies
809
views
pairwise comparison with ballgown
ballgown
6.6 years ago behnam.derakhshani • 0
0
votes
0
replies
948
views
Model problem using ballgown
ballgown linear models
6.6 years ago Yong Li ▴ 50
0
votes
1
reply
1.0k
views
ballgown time course design and command confirmation
ballgown stattest multiple time points
6.6 years ago yadongxue • 0
0
votes
3
replies
2.0k
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
814
views
Ballgown data read error
ballgown software error
6.6 years ago amy16 • 0
5
votes
14
replies
8.0k
views
DESeq2 vs Ballgown results
ballgown deseq2
6.7 years ago • updated 6.6 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
946
views
Subset functionin R
R ballgown rnaseq
6.8 years ago amy16 • 0
0
votes
0
replies
917
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 6.8 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 6.8 years ago by ▴ 210 • written 6.8 years ago by ▴ 10
1
vote
2
replies
1.7k
views
Error in reading ballgown object
R ballgown
updated 6.8 years ago by ▴ 210 • written 6.8 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 6.9 years ago by ▴ 210 • written 7.7 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Differential Expression Analysis with unbalanced batches without replication bet by Thili • 0
Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…
Comment: Problem at champ.load by andrew.gibbons • 0
I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…
Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column by GV Yoshikawa • 0
Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Answer: Differential Expression Analysis with unbalanced batches without replication bet by Gordon Smyth 51k
> Is there an alternative model or approach in tools like edgeR, limma-voom, or DESeq2 or any other that can handle confounded batch effect…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected. by Adam • 0
I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…
Votes
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
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