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Showing :
Ballgown
•
reset
0
votes
4
replies
376
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
12 weeks ago
candacenewcome
• 0
1
vote
2
replies
409
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2
DGEanalysis
ballgown
Ballgown
DiseasedvsNormal
9 months ago
Bushra
• 0
0
votes
1
reply
952
views
is.null(pData) | class(pData) == "data.frame" is not TRUE
ballgown
updated 2.6 years ago by
Hervé Pagès
16k • written 2.7 years ago by
merden1603
• 0
0
votes
1
reply
972
views
Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 3.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 3.5 years ago by
katrinegraversen
• 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
Alyssa Frazee
▴ 210 • written 3.6 years ago by
pushgct
• 0
0
votes
3
replies
1.4k
views
StringTie output as Ballgown input
ballgown
StringTie
galaxy
rnaseq
updated 22 months ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
lakshmi9c
• 0
1
vote
2
replies
870
views
Regularization of ballgown object on Limma
limma
ballgown
RNA-seq
4.2 years ago
komuracom16
• 0
0
votes
0
replies
791
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
647
views
ballgown -- how is statistical test performed
ballgown
rna-seq
4.6 years ago
michael
• 0
0
votes
0
replies
601
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
Alyssa Frazee
▴ 210 • written 5.3 years ago by
aaubry89
• 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
Gordon Smyth
50k • written 5.3 years ago by
IRAIA.MAIALEN
• 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
Mike Smith
★ 6.5k • written 5.5 years ago by
Mithil Gaikwad
• 0
0
votes
0
replies
820
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r
ballgown
5.5 years ago
viv333chavan
• 0
0
votes
1
reply
778
views
Understanding the output from Ballgown for DE
changes
ballgown
5.6 years ago
amy16
• 0
0
votes
0
replies
778
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
2
replies
931
views
Including batch effects in the differential expression of gene analysis
ballgown
new tuxedo pipleine
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
amy16
• 0
0
votes
1
reply
1.8k
views
Issue using ballgown
software error
ballgown
genomeinfodbdata
genomeinfodb
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
dualeahmed
• 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
773
views
Ballgown Plotmeans problem
ballgown
5.7 years ago
new_user
• 0
1
vote
1
reply
769
views
ballgown bamfiles vector
ballgown
5.7 years ago
jac1318
• 0
0
votes
0
replies
961
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
983
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
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
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
977
views
pair wise ballgown
ballgown
differential expression
5.8 years ago
zoe.ward
• 0
0
votes
1
reply
946
views
Interactions and contrasts for DE analysis in ballgown
ballgown
R
RNAseq
DE
interactions
updated 5.8 years ago by
James W. MacDonald
65k • written 5.8 years ago by
khill33
• 0
0
votes
1
reply
860
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
James W. MacDonald
65k • written 5.9 years ago by
marasodi
• 0
1
vote
2
replies
988
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
James W. MacDonald
65k • written 6.0 years ago by
ryanding2003
• 0
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
714
views
pairwise comparison with ballgown
ballgown
6.0 years ago
behnam.derakhshani
• 0
0
votes
0
replies
830
views
Model problem using ballgown
ballgown
linear models
6.0 years ago
Yong Li
▴ 50
0
votes
1
reply
900
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
James W. MacDonald
65k • written 6.1 years ago by
amy16
• 0
0
votes
0
replies
733
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
James W. MacDonald
65k • written 6.1 years ago by
ag1805x
▴ 80
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
806
views
Subset functionin R
R
ballgown
rnaseq
6.2 years ago
amy16
• 0
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
820
views
Accessing the assembly data-output
R
rnaseq
ballgown
6.2 years ago
amy16
• 0
1
vote
5
replies
2.4k
views
Error in stattest function
R
rnaseq
Ballgown
updated 2.9 years ago by
muhammadharoon974
• 0 • written 6.2 years ago by
amy16
• 0
1
vote
2
replies
1.5k
views
Error in reading ballgown object
R
ballgown
updated 6.3 years ago by
Alyssa Frazee
▴ 210 • written 6.3 years ago by
amy16
• 0
1
vote
3
replies
2.6k
views
Multiple pairwise comparisons in ballgown
ballgown
updated 6.3 years ago by
Alyssa Frazee
▴ 210 • written 6.3 years ago by
rachael.detar
▴ 10
1
vote
1
reply
1.4k
views
RNA-seq for DGE
stringtie
illumina
hisat2
ballgown
updated 6.4 years ago by
k.vitting.seerup
▴ 120 • written 6.4 years ago by
amy16
• 0
2
votes
0
replies
983
views
p-values, q-values, duplicated entries in output - ballgown
ballgown
rna-seq
q value
r
6.6 years ago
mkhasin
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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