Showing : ballgown • reset
0
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4
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357
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Ballgown error in scan for c.tab files
ballgown RNASeq
11 weeks ago • updated 10 weeks ago candacenewcome • 0
1
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2
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396
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DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
9 months ago Bushra • 0
0
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1
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944
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is.null(pData) | class(pData) == "data.frame" is not TRUE
ballgown
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
1
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5
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2.4k
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Error in stattest function
R rnaseq Ballgown
updated 2.9 years ago by • 0 • written 6.2 years ago by • 0
0
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1
reply
967
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Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 3.5 years ago by ★ 1.0k • written 3.5 years ago by • 0
0
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0
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1.3k
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HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
3.5 years ago ra711 • 0
0
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1
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1.2k
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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 3.6 years ago by ▴ 210 • written 3.6 years ago by • 0
0
votes
3
replies
1.4k
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StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 22 months ago by ★ 3.9k • written 3.7 years ago by • 0
1
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2
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863
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Regularization of ballgown object on Limma
limma ballgown RNA-seq
4.2 years ago komuracom16 • 0
0
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0
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780
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Is the ballgownrsem function still supported?
ballgown rsem iranges
4.3 years ago YH • 0
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0
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639
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ballgown -- how is statistical test performed
ballgown rna-seq
4.6 years ago michael • 0
0
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0
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594
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ballgown: how to test for DE for my experimental setup
ballgown rna-seq
4.6 years ago michael • 0
0
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0
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1.7k
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
5.0 years ago fatimarasool135 • 0
1
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2
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1.1k
views
Ballgown Error .null(pData) | class(pData) == "data.frame" are not all TRUE
software error ballgown
updated 5.2 years ago by ▴ 210 • written 5.2 years ago by • 0
2
votes
2
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1.5k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 5.2 years ago by 50k • written 5.2 years ago by • 0
0
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0
replies
1.1k
views
Error while loading the data structrure in the ballgown tool
ballgown rnaseq differential gene expression new tuxedo pipleine
5.4 years ago Mithil Gaikwad • 0
0
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1
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2.1k
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Can not install packages
ballgown genefilter RskittleBrewer
updated 5.4 years ago by ★ 6.5k • written 5.4 years ago by • 0
0
votes
0
replies
811
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Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r ballgown
5.5 years ago viv333chavan • 0
0
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1
reply
771
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Understanding the output from Ballgown for DE
changes ballgown
5.5 years ago amy16 • 0
0
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0
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770
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R script to fix the error in dataframe when using ballgown for differentially expression analysis
r ballgown code error
5.5 years ago amy16 • 0
0
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3
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1.5k
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Ballgown differential expression by exon problem
ballgown
5.6 years ago new_user • 0
0
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1
reply
1.8k
views
Issue using ballgown
software error ballgown genomeinfodbdata genomeinfodb
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
0
votes
2
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927
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Including batch effects in the differential expression of gene analysis
ballgown new tuxedo pipleine
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
1
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1
reply
762
views
ballgown bamfiles vector
ballgown
5.7 years ago • updated 5.6 years ago jac1318 • 0
0
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1
reply
767
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Ballgown Plotmeans problem
ballgown
5.6 years ago new_user • 0
0
votes
0
replies
951
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
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2.0k
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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
0
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1
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974
views
Error loading data, pheno_data names in 1st column do not match ballgown/sample dir names.
ballgown
5.8 years ago harris • 0
1
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0
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1.2k
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covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
5.8 years ago justinjj ▴ 10
0
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0
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972
views
pair wise ballgown
ballgown differential expression
5.8 years ago zoe.ward • 0
0
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1
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942
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Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
0
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1
reply
854
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Ballgown for differential expressed genes
ballgown
5.9 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 5.9 years ago by 65k • written 5.9 years ago by • 0
1
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2
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978
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RNA-Seq differential analysis with ballgown, getting more significantly deferentially expressed genes than significantly deferentially expressed tra…
ballgown
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
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0
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1.8k
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RNA-seq with hisat2+stringtie+ballgown
hisat2 stringtie ballgown RNAseq
6.2 years ago • updated 5.9 years ago Nancy ▴ 10
0
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0
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1.3k
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Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.0 years ago vharshavardhanan • 0
0
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0
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707
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pairwise comparison with ballgown
ballgown
6.0 years ago behnam.derakhshani • 0
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0
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822
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Model problem using ballgown
ballgown linear models
6.0 years ago Yong Li ▴ 50
0
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1
reply
892
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ballgown time course design and command confirmation
ballgown stattest multiple time points
6.0 years ago yadongxue • 0
0
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3
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1.9k
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Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.0 years ago by 65k • written 6.0 years ago by • 0
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0
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724
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Ballgown data read error
ballgown software error
6.0 years ago amy16 • 0
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14
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7.4k
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DESeq2 vs Ballgown results
ballgown deseq2
6.1 years ago CE ▴ 20
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1.3k
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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 6.1 years ago by 65k • written 6.1 years ago by ▴ 80
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4
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1.7k
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error reading ballgown object
R ballgown
6.2 years ago l.j.leach • 0
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0
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796
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Subset functionin R
R ballgown rnaseq
6.2 years ago amy16 • 0
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0
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815
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Accessing the assembly data-output
R rnaseq ballgown
6.2 years ago amy16 • 0
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3
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1.8k
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error in filtering genes with rowVars(gexpr(bg_chrX)) >1
genefilter ballgown
updated 6.3 years ago by • 0 • written 6.7 years ago by • 0
1
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3
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2.6k
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Multiple pairwise comparisons in ballgown
ballgown
updated 6.3 years ago by ▴ 210 • written 6.3 years ago by ▴ 10
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2
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1.5k
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Error in reading ballgown object
R ballgown
updated 6.3 years ago by ▴ 210 • written 6.3 years ago by • 0
0
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7
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2.5k
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Handling both technical and biological replicates in Ballgown
ballgown biologicalreplicates technical replicates stringtie
updated 6.4 years ago by ▴ 210 • written 7.1 years ago by • 0
50 results • Page 1 of 1
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Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Comment: A ComBat-seq issue: the covariates are confounded by W. Evan Johnson ▴ 850
This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…
Answer: Different number of exons in reference genome affects DEXSeq analysis by Alejandro Reyes ★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Answer: Adding columns to DEXSeqResults object by Alejandro Reyes ★ 1.9k
I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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