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ballgown
•
reset
0
votes
4
replies
370
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
12 weeks ago • updated 11 weeks ago
candacenewcome
• 0
1
vote
2
replies
400
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2
DGEanalysis
ballgown
Ballgown
DiseasedvsNormal
9 months ago
Bushra
• 0
0
votes
1
reply
948
views
is.null(pData) | class(pData) == "data.frame" is not TRUE
ballgown
updated 2.6 years ago by
Hervé Pagès
16k • written 2.6 years ago by
merden1603
• 0
0
votes
1
reply
970
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
867
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
4.3 years ago
YH
• 0
0
votes
0
replies
643
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
Alyssa Frazee
▴ 210 • written 5.2 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
5.4 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
Mike Smith
★ 6.5k • written 5.5 years ago by
Mithil Gaikwad
• 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
5.5 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
2
replies
929
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
770
views
Ballgown Plotmeans problem
ballgown
5.7 years ago
new_user
• 0
1
vote
1
reply
767
views
ballgown bamfiles vector
ballgown
5.7 years ago
jac1318
• 0
0
votes
0
replies
956
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
979
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
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
James W. MacDonald
65k • written 5.8 years ago by
khill33
• 0
0
votes
1
reply
856
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
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
James W. MacDonald
65k • written 5.9 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
710
views
pairwise comparison with ballgown
ballgown
6.0 years ago
behnam.derakhshani
• 0
0
votes
0
replies
824
views
Model problem using ballgown
ballgown
linear models
6.0 years ago
Yong Li
▴ 50
0
votes
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
James W. MacDonald
65k • written 6.0 years ago by
amy16
• 0
0
votes
0
replies
728
views
Ballgown data read error
ballgown
software error
6.0 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
800
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
818
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
Answer: Citation for edgeR user guide
by
Gordon Smyth
50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class?
by
James W. MacDonald
65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp
by
clacarion
• 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp
by
clacarion
• 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Votes
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
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