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thelovelab
/
fishpond
Differential expression and allelic analysis, nonparametric statistics
https://thelovelab.github.io/fishpond
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Issues with loadFry() ('x@assays' is not parallel to 'x')
#38
AnnaAMonaco
closed
1 month ago
4
Unused argument (diffAI = TRUE)
#37
zhangjy859
closed
7 months ago
5
Have all 0 LFC for all infReps, remove these first
#36
zhangjy859
closed
7 months ago
5
Wrong index in randomSamplesToRemove()
#35
smlchen
closed
1 year ago
4
Add definition of InfRV to computeInfRV
#34
mikelove
closed
1 year ago
0
gene_ids after summarising counts with loadFry
#33
ChristelKrueger
closed
1 year ago
5
Feat: Adding more pre-defined output formats for the loadFry function
#32
DongzeHE
closed
1 year ago
1
Fix bug salmonEC: internally address indexing discrepancy
#31
jgilis
closed
1 year ago
1
How to output the scaled counts for each sample
#30
biozzq
closed
1 year ago
3
Allow importing of gene names with underscores
#29
JosephLalli
closed
1 year ago
6
alevinEC test
#28
jgilis
closed
2 years ago
1
Better column names
#27
jgilis
closed
2 years ago
3
R CMD check WARNING: Requires (indirectly) orphaned package: ‘gtools’
#26
DongzeHE
closed
2 years ago
3
Extend to ordinal conditions
#25
JosephLalli
opened
2 years ago
7
Using loadFry for HTO quantifications
#24
jeremymsimon
closed
2 years ago
5
fix Description
#23
jgilis
closed
2 years ago
0
Update yml
#22
jgilis
closed
2 years ago
1
salmonEC and alevinEC updates and tests
#21
jgilis
closed
2 years ago
4
Fix a bug for non-USA mode
#20
DongzeHE
closed
2 years ago
0
Allelic plots should offer to customize allelic labels
#19
mikelove
closed
2 years ago
0
salmon-EC
#18
jgilis
closed
2 years ago
3
alevin-EC
#17
jgilis
closed
2 years ago
3
plotInfReps y axis mislabel
#16
qxxxd
closed
2 years ago
2
make output format robust
#15
DongzeHE
closed
2 years ago
1
One-sample t-test for paired design
#14
mikelove
closed
2 years ago
1
expanded argument nonzero, and changed verbose -> quiet
#13
DongzeHE
closed
2 years ago
0
now ships with enough example cells/genes to pass velociraptor test
#12
Varix
closed
2 years ago
0
Redesigned loadFry function
#11
DongzeHE
closed
2 years ago
2
Added native support for Velociraptor
#10
Varix
closed
2 years ago
1
Adds ability to include an "unspliced" assay in return from loadFry()
#9
lianos
closed
3 years ago
8
correct fromJSON argument
#8
DongzeHE
closed
3 years ago
2
update loadFry function
#7
DongzeHE
closed
3 years ago
4
add loadFry related code and example
#6
DongzeHE
closed
3 years ago
2
matrixStats::rowRanks(): Specify argument 'ties.method = "max"' to avoid being affected by future updates
#5
HenrikBengtsson
closed
3 years ago
3
Error in infRepError(infRepIdx) : there are no inferential replicates in the assays of 'y'
#4
sunliang3361
closed
4 years ago
1
Error in dbFileConnect(file)
#3
sunliang3361
closed
4 years ago
2
[WIP] adding tiers parser
#2
k3yavi
closed
4 years ago
0
support of sparsed Matrix output of alevin
#1
DrHogart
closed
4 years ago
6