Showing : ballgown • reset
0
votes
4
replies
377
views
Ballgown error in scan for c.tab files
ballgown RNASeq
12 weeks ago candacenewcome • 0
1
vote
2
replies
410
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
9 months ago Bushra • 0
0
votes
1
reply
953
views
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
replies
2.4k
views
Error in stattest function
R rnaseq Ballgown
updated 2.9 years ago by • 0 • written 6.2 years ago by • 0
0
votes
1
reply
975
views
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
votes
0
replies
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
votes
1
reply
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 3.6 years ago by ▴ 210 • written 3.6 years ago by • 0
0
votes
3
replies
1.4k
views
StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 22 months ago by ★ 3.9k • written 3.7 years ago by • 0
1
vote
2
replies
871
views
Regularization of ballgown object on Limma
limma ballgown RNA-seq
4.2 years ago komuracom16 • 0
0
votes
0
replies
792
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
4.4 years ago • updated 4.3 years ago YH • 0
0
votes
0
replies
649
views
ballgown -- how is statistical test performed
ballgown rna-seq
4.6 years ago michael • 0
0
votes
0
replies
603
views
ballgown: how to test for DE for my experimental setup
ballgown rna-seq
4.6 years ago michael • 0
0
votes
0
replies
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
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
1.5k
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
822
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r ballgown
5.5 years ago viv333chavan • 0
0
votes
1
reply
780
views
Understanding the output from Ballgown for DE
changes ballgown
5.6 years ago amy16 • 0
0
votes
0
replies
779
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
1.5k
views
Ballgown differential expression by exon problem
ballgown
5.6 years ago new_user • 0
0
votes
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
replies
932
views
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
vote
1
reply
772
views
ballgown bamfiles vector
ballgown
5.7 years ago jac1318 • 0
0
votes
1
reply
775
views
Ballgown Plotmeans problem
ballgown
5.7 years ago new_user • 0
0
votes
0
replies
962
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
vote
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
5.8 years ago kicheol.kim • 0
0
votes
1
reply
986
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
vote
0
replies
1.2k
views
covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
5.8 years ago justinjj ▴ 10
0
votes
0
replies
980
views
pair wise ballgown
ballgown differential expression
5.8 years ago zoe.ward • 0
0
votes
1
reply
947
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
1
reply
862
views
Ballgown for differential expressed genes
ballgown
5.9 years ago marasodi • 0
0
votes
2
replies
1.0k
views
Ballgown for differential expressed genes
ballgown
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
1
vote
2
replies
996
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 65k • written 6.0 years ago by • 0
0
votes
0
replies
1.8k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2 stringtie ballgown RNAseq
6.2 years ago • updated 6.0 years ago Nancy ▴ 10
0
votes
0
replies
1.3k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.0 years ago vharshavardhanan • 0
0
votes
0
replies
715
views
pairwise comparison with ballgown
ballgown
6.0 years ago behnam.derakhshani • 0
0
votes
0
replies
831
views
Model problem using ballgown
ballgown linear models
6.0 years ago Yong Li ▴ 50
0
votes
1
reply
901
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 65k • written 6.1 years ago by • 0
0
votes
0
replies
734
views
Ballgown data read error
ballgown software error
6.1 years ago amy16 • 0
5
votes
14
replies
7.4k
views
DESeq2 vs Ballgown results
ballgown deseq2
6.1 years ago CE ▴ 20
1
vote
1
reply
1.3k
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 6.1 years ago by 65k • written 6.1 years ago by ▴ 80
2
votes
4
replies
1.7k
views
error reading ballgown object
R ballgown
6.2 years ago l.j.leach • 0
0
votes
0
replies
808
views
Subset functionin R
R ballgown rnaseq
6.2 years ago amy16 • 0
0
votes
0
replies
823
views
Accessing the assembly data-output
R rnaseq ballgown
6.2 years ago amy16 • 0
0
votes
3
replies
1.8k
views
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
vote
3
replies
2.6k
views
Multiple pairwise comparisons in ballgown
ballgown
updated 6.3 years ago by ▴ 210 • written 6.3 years ago by ▴ 10
1
vote
2
replies
1.5k
views
Error in reading ballgown object
R ballgown
updated 6.3 years ago by ▴ 210 • written 6.3 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 6.4 years ago by ▴ 210 • written 7.1 years ago by • 0
50 results • Page 1 of 1
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 30
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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