Showing : Ballgown • reset
0
votes
4
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372
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Ballgown error in scan for c.tab files
ballgown RNASeq
12 weeks ago • updated 11 weeks ago candacenewcome • 0
1
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2
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401
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DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
9 months ago Bushra • 0
0
votes
1
reply
949
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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
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
970
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
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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
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868
views
Regularization of ballgown object on Limma
limma ballgown RNA-seq
4.2 years ago komuracom16 • 0
0
votes
0
replies
787
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
4.4 years ago • updated 4.3 years ago YH • 0
0
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0
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644
views
ballgown -- how is statistical test performed
ballgown rna-seq
4.6 years ago michael • 0
0
votes
0
replies
599
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 5.2 years ago by ▴ 210 • written 5.2 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
5.4 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
817
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r ballgown
5.5 years ago viv333chavan • 0
0
votes
1
reply
774
views
Understanding the output from Ballgown for DE
changes ballgown
5.6 years ago amy16 • 0
0
votes
0
replies
774
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
929
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
767
views
ballgown bamfiles vector
ballgown
5.7 years ago jac1318 • 0
0
votes
1
reply
771
views
Ballgown Plotmeans problem
ballgown
5.7 years ago new_user • 0
0
votes
0
replies
958
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
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
980
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
975
views
pair wise ballgown
ballgown differential expression
5.8 years ago zoe.ward • 0
0
votes
1
reply
945
views
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
857
views
Ballgown for differential expressed genes
ballgown
5.9 years ago marasodi • 0
0
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2
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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
984
views
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
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
710
views
pairwise comparison with ballgown
ballgown
6.0 years ago behnam.derakhshani • 0
0
votes
0
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827
views
Model problem using ballgown
ballgown linear models
6.0 years ago Yong Li ▴ 50
0
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1
reply
897
views
ballgown time course design and command confirmation
ballgown stattest multiple time points
6.0 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 6.0 years ago by 65k • written 6.1 years ago by • 0
0
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0
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730
views
Ballgown data read error
ballgown software error
6.1 years ago amy16 • 0
5
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14
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7.4k
views
DESeq2 vs Ballgown results
ballgown deseq2
6.1 years ago CE ▴ 20
1
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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
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4
replies
1.7k
views
error reading ballgown object
R ballgown
6.2 years ago l.j.leach • 0
0
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0
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800
views
Subset functionin R
R ballgown rnaseq
6.2 years ago amy16 • 0
0
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0
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818
views
Accessing the assembly data-output
R rnaseq ballgown
6.2 years ago amy16 • 0
0
votes
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 6.7 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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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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