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ballgown
•
reset
0
votes
4
replies
312
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
8 weeks ago • updated 7 weeks ago
candacenewcome
• 0
1
vote
2
replies
377
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2
DGEanalysis
ballgown
Ballgown
DiseasedvsNormal
8 months ago
Bushra
• 0
0
votes
1
reply
921
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
1
vote
5
replies
2.4k
views
Error in stattest function
R
rnaseq
Ballgown
updated 2.8 years ago by
muhammadharoon974
• 0 • written 6.2 years ago by
amy16
• 0
0
votes
1
reply
941
views
Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 3.4 years ago by
Leonardo Collado Torres
★ 1.0k • written 3.4 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
3.5 years ago
ra711
• 0
0
votes
1
reply
1.1k
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 3.5 years ago by
Alyssa Frazee
▴ 210 • written 3.5 years ago by
pushgct
• 0
0
votes
3
replies
1.4k
views
StringTie output as Ballgown input
ballgown
StringTie
galaxy
rnaseq
updated 21 months ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
lakshmi9c
• 0
1
vote
2
replies
838
views
Regularization of ballgown object on Limma
limma
ballgown
RNA-seq
4.2 years ago
komuracom16
• 0
0
votes
0
replies
763
views
Is the ballgownrsem function still supported?
ballgown
rsem
iranges
4.3 years ago
YH
• 0
0
votes
0
replies
625
views
ballgown -- how is statistical test performed
ballgown
rna-seq
4.5 years ago
michael
• 0
0
votes
0
replies
579
views
ballgown: how to test for DE for my experimental setup
ballgown
rna-seq
4.5 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 5.2 years ago by
Gordon Smyth
50k • written 5.2 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 5.4 years ago by
Mike Smith
★ 6.5k • written 5.4 years ago by
Mithil Gaikwad
• 0
0
votes
0
replies
800
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r
ballgown
5.4 years ago
viv333chavan
• 0
0
votes
1
reply
756
views
Understanding the output from Ballgown for DE
changes
ballgown
5.5 years ago
amy16
• 0
0
votes
0
replies
757
views
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
votes
3
replies
1.5k
views
Ballgown differential expression by exon problem
ballgown
5.6 years ago • updated 5.5 years ago
new_user
• 0
0
votes
1
reply
1.8k
views
Issue using ballgown
software error
ballgown
genomeinfodbdata
genomeinfodb
updated 5.5 years ago by
James W. MacDonald
65k • written 5.5 years ago by
dualeahmed
• 0
0
votes
2
replies
914
views
Including batch effects in the differential expression of gene analysis
ballgown
new tuxedo pipleine
updated 5.5 years ago by
James W. MacDonald
65k • written 5.5 years ago by
amy16
• 0
1
vote
1
reply
751
views
ballgown bamfiles vector
ballgown
5.6 years ago
jac1318
• 0
0
votes
1
reply
754
views
Ballgown Plotmeans problem
ballgown
5.6 years ago
new_user
• 0
0
votes
0
replies
936
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown
rsem
iranges
5.7 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
5.7 years ago
kicheol.kim
• 0
0
votes
1
reply
962
views
Error loading data, pheno_data names in 1st column do not match ballgown/sample dir names.
ballgown
5.7 years ago
harris
• 0
1
vote
0
replies
1.2k
views
covariate vs adjustvars
ballgown
rnaseq
differential gene expression
tuxedo
5.7 years ago
justinjj
▴ 10
0
votes
0
replies
957
views
pair wise ballgown
ballgown
differential expression
5.8 years ago
zoe.ward
• 0
0
votes
1
reply
923
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
837
views
Ballgown for differential expressed genes
ballgown
5.8 years ago
marasodi
• 0
0
votes
2
replies
991
views
Ballgown for differential expressed genes
ballgown
updated 5.8 years ago by
James W. MacDonald
65k • written 5.8 years ago by
marasodi
• 0
1
vote
2
replies
957
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
1.8k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2
stringtie
ballgown
RNAseq
6.1 years ago • updated 5.9 years ago
Nancy
▴ 10
0
votes
0
replies
1.3k
views
Ballgown data processing error
Ballgown
Stringtie
DEG
rnaseq
5.9 years ago
vharshavardhanan
• 0
0
votes
0
replies
695
views
pairwise comparison with ballgown
ballgown
5.9 years ago
behnam.derakhshani
• 0
0
votes
0
replies
809
views
Model problem using ballgown
ballgown
linear models
6.0 years ago
Yong Li
▴ 50
0
votes
1
reply
876
views
ballgown time course design and command confirmation
ballgown
stattest
multiple time points
6.0 years ago
yadongxue
• 0
0
votes
3
replies
1.8k
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
712
views
Ballgown data read error
ballgown
software error
6.0 years ago
amy16
• 0
5
votes
14
replies
7.3k
views
DESeq2 vs Ballgown results
ballgown
deseq2
6.0 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 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
ag1805x
▴ 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
778
views
Subset functionin R
R
ballgown
rnaseq
6.2 years ago
amy16
• 0
0
votes
0
replies
799
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 6.2 years ago by
importantrubbish
• 0 • written 6.6 years ago by
fubeide
• 0
1
vote
3
replies
2.6k
views
Multiple pairwise comparisons in ballgown
ballgown
updated 6.2 years ago by
Alyssa Frazee
▴ 210 • written 6.2 years ago by
rachael.detar
▴ 10
1
vote
2
replies
1.5k
views
Error in reading ballgown object
R
ballgown
updated 6.2 years ago by
Alyssa Frazee
▴ 210 • written 6.2 years ago by
amy16
• 0
0
votes
7
replies
2.5k
views
Handling both technical and biological replicates in Ballgown
ballgown
biologicalreplicates
technical replicates
stringtie
updated 6.3 years ago by
Alyssa Frazee
▴ 210 • written 7.1 years ago by
linda.boshans
• 0
50 results • Page
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Recent ...
Replies
Comment: error when using M-values in ChAMP
by
hortenseguillaume96
• 0
Hello Tian, I'd like to get the M-values matrix so that I can carry out a linear regression study. However, when I apply the champ.load fu…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
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