thelovelab/fishpond issues and pull requests

#38 - Issues with loadFry() ('x@assays' is not parallel to 'x')

Issue - State: closed - Opened by AnnaAMonaco 3 months ago - 4 comments

#37 - Unused argument (diffAI = TRUE)

Issue - State: closed - Opened by zhangjy859 9 months ago - 5 comments

#36 - Have all 0 LFC for all infReps, remove these first

Issue - State: closed - Opened by zhangjy859 11 months ago - 5 comments

#35 - Wrong index in randomSamplesToRemove()

Issue - State: closed - Opened by smlchen over 1 year ago - 4 comments

#34 - Add definition of InfRV to computeInfRV

Issue - State: closed - Opened by mikelove over 1 year ago

#33 - gene_ids after summarising counts with loadFry

Issue - State: closed - Opened by ChristelKrueger over 1 year ago - 5 comments

#32 - Feat: Adding more pre-defined output formats for the loadFry function

Pull Request - State: closed - Opened by DongzeHE almost 2 years ago - 1 comment

#31 - Fix bug salmonEC: internally address indexing discrepancy

Pull Request - State: closed - Opened by jgilis almost 2 years ago - 1 comment

#30 - How to output the scaled counts for each sample

Issue - State: closed - Opened by biozzq almost 2 years ago - 3 comments

#29 - Allow importing of gene names with underscores

Pull Request - State: closed - Opened by JosephLalli about 2 years ago - 6 comments

#28 - alevinEC test

Pull Request - State: closed - Opened by jgilis about 2 years ago - 1 comment

#27 - Better column names

Pull Request - State: closed - Opened by jgilis about 2 years ago - 3 comments

#26 - R CMD check WARNING: Requires (indirectly) orphaned package: ‘gtools’

Issue - State: closed - Opened by DongzeHE over 2 years ago - 3 comments

#25 - Extend to ordinal conditions

Issue - State: open - Opened by JosephLalli over 2 years ago - 7 comments

#24 - Using loadFry for HTO quantifications

Issue - State: closed - Opened by jeremymsimon over 2 years ago - 5 comments

#23 - fix Description

Pull Request - State: closed - Opened by jgilis over 2 years ago

#22 - Update yml

Pull Request - State: closed - Opened by jgilis over 2 years ago - 1 comment

#21 - salmonEC and alevinEC updates and tests

Pull Request - State: closed - Opened by jgilis over 2 years ago - 4 comments

#20 - Fix a bug for non-USA mode

Pull Request - State: closed - Opened by DongzeHE over 2 years ago

#19 - Allelic plots should offer to customize allelic labels

Issue - State: closed - Opened by mikelove over 2 years ago

#18 - salmon-EC

Pull Request - State: closed - Opened by jgilis over 2 years ago - 3 comments

#17 - alevin-EC

Pull Request - State: closed - Opened by jgilis over 2 years ago - 3 comments

#16 - plotInfReps y axis mislabel

Issue - State: closed - Opened by qxxxd over 2 years ago - 2 comments

#15 - make output format robust

Pull Request - State: closed - Opened by DongzeHE over 2 years ago - 1 comment

#14 - One-sample t-test for paired design

Issue - State: closed - Opened by mikelove over 2 years ago - 1 comment
Labels: enhancement

#13 - expanded argument nonzero, and changed verbose -> quiet

Pull Request - State: closed - Opened by DongzeHE about 3 years ago

#12 - now ships with enough example cells/genes to pass velociraptor test

Pull Request - State: closed - Opened by Varix about 3 years ago

#11 - Redesigned loadFry function

Pull Request - State: closed - Opened by DongzeHE about 3 years ago - 2 comments

#10 - Added native support for Velociraptor

Pull Request - State: closed - Opened by Varix about 3 years ago - 1 comment

#9 - Adds ability to include an "unspliced" assay in return from loadFry()

Pull Request - State: closed - Opened by lianos about 3 years ago - 8 comments

#8 - correct fromJSON argument

Pull Request - State: closed - Opened by DongzeHE over 3 years ago - 2 comments

#7 - update loadFry function

Pull Request - State: closed - Opened by DongzeHE over 3 years ago - 4 comments

#6 - add loadFry related code and example