hugheylab/simphony issues and pull requests

#83 - lintr found issues with code

Issue - State: closed - Opened by github-actions[bot] almost 2 years ago
Labels: lint

#82 - lintr found issues with code

Issue - State: closed - Opened by github-actions[bot] over 2 years ago
Labels: lint

#81 - lintr found issues with code

Issue - State: closed - Opened by github-actions[bot] over 2 years ago
Labels: lint

#80 - lintr found issues with code

Issue - State: closed - Opened by github-actions[bot] over 2 years ago
Labels: lint

#79 - lintr found issues with code

Issue - State: closed - Opened by github-actions[bot] over 2 years ago
Labels: lint

#78 - lintr found issues with code

Issue - State: closed - Opened by github-actions[bot] over 2 years ago
Labels: lint

#77 - lintr found issues with code

Issue - State: closed - Opened by github-actions[bot] over 2 years ago
Labels: lint

#76 - lintr found issues with code

Issue - State: closed - Opened by github-actions[bot] over 2 years ago
Labels: lint

#75 - Update workflow files

Pull Request - State: closed - Opened by JSchoenbachler about 3 years ago - 4 comments

#74 - Remove circleCI and add github actions

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

#73 - Change globalVariables usage

Pull Request - State: closed - Opened by JSchoenbachler over 3 years ago - 5 comments

#72 - Add covr install and remove from suggests

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

#71 - Update to R 4.1.0

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

#70 - Change check failures step to calculate coverage

Pull Request - State: closed - Opened by JSchoenbachler over 3 years ago - 1 comment

#69 - Docker Image to R 4.0.5 and Main branch checking

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

#68 - Update CircleCI run to R 4.0.2

Pull Request - State: closed - Opened by JSchoenbachler about 4 years ago - 2 comments

#67 - Exclude NEWS.md

Pull Request - State: closed - Opened by JSchoenbachler over 4 years ago - 6 comments

#66 - Update for Fix with directory drat deployment

Pull Request - State: closed - Opened by JSchoenbachler over 4 years ago - 1 comment

#65 - Update for hash checking and code coverage % uploading

Pull Request - State: closed - Opened by JSchoenbachler over 4 years ago - 1 comment

#64 - Update Config to Add Coverage %

Pull Request - State: closed - Opened by JSchoenbachler over 4 years ago - 1 comment

#63 - added bernoulli and poisson sampling.

Pull Request - State: closed - Opened by jakejh over 5 years ago

#62 - updated config for circleci, so that package tar.gz file gets added t…

Pull Request - State: closed - Opened by jakejh over 5 years ago

#61 - updated readme with published dois.

Pull Request - State: closed - Opened by jakejh over 5 years ago

#60 - Add example of custom rhyfunc

Pull Request - State: closed - Opened by ZackAttack614 over 5 years ago

#59 - Ci

Pull Request - State: closed - Opened by ZackAttack614 over 5 years ago
Labels: enhancement

#58 - Documentation

Pull Request - State: closed - Opened by ZackAttack614 over 5 years ago - 3 comments

#57 - Examples

Pull Request - State: closed - Opened by jakejh over 5 years ago

#56 - refactored some code and documentation.

Pull Request - State: closed - Opened by jakejh over 5 years ago

#55 - Fix CircleCI configuration

Pull Request - State: closed - Opened by ZackAttack614 over 5 years ago

#54 - Time dependence

Pull Request - State: closed - Opened by jakejh over 5 years ago

#53 - Time dependence

Pull Request - State: closed - Opened by ZackAttack614 over 5 years ago

#52 - Add period to featureGroups Argument

Issue - State: closed - Opened by ZackAttack614 almost 6 years ago
Labels: enhancement

#51 - Elaborate on Vignette(s)

Issue - State: closed - Opened by ZackAttack614 almost 6 years ago
Labels: enhancement

#50 - Add Time Range Argument to Simphony Call

Issue - State: closed - Opened by ZackAttack614 almost 6 years ago - 1 comment
Labels: enhancement

#49 - Add Dampening Term to Rhythms

Issue - State: closed - Opened by ZackAttack614 almost 6 years ago
Labels: enhancement

#48 - Rework

Pull Request - State: closed - Opened by ZackAttack614 almost 6 years ago

#47 - Why do we force sd > 0?

Issue - State: closed - Opened by ZackAttack614 almost 6 years ago - 1 comment
Labels: invalid, question

#46 - Remove empirically estimated distribution of rhythm amplitudes

Issue - State: closed - Opened by jakejh almost 6 years ago

#45 - Rename variables to be agnostic to the type of measurement

Issue - State: closed - Opened by jakejh almost 6 years ago - 6 comments
Labels: decision

#44 - Empirical

Pull Request - State: closed - Opened by jakejh almost 6 years ago - 1 comment

#43 - Need for speed

Pull Request - State: closed - Opened by jakejh about 6 years ago

#42 - Unit testing

Pull Request - State: closed - Opened by ZackAttack614 about 6 years ago

#41 - Polish

Pull Request - State: closed - Opened by jakejh about 6 years ago

#40 - fixed another bug in getExpectedExpr.

Pull Request - State: closed - Opened by jakejh about 6 years ago
Labels: bug

#39 - fix cryptic behavior of getExpectedExpr function.

Pull Request - State: closed - Opened by jakejh about 6 years ago
Labels: bug

#38 - Polish

Pull Request - State: closed - Opened by jakejh about 6 years ago

#37 - Polish

Pull Request - State: closed - Opened by jakejh about 6 years ago
Labels: minor

#36 - Fix roxygen, unit test, and logical errors.

Pull Request - State: closed - Opened by ZackAttack614 about 6 years ago - 5 comments

#35 - Polish

Pull Request - State: closed - Opened by jakejh about 6 years ago - 1 comment
Labels: enhancement

#34 - Polish

Pull Request - State: closed - Opened by jakejh about 6 years ago
Labels: minor

#33 - Remove unnecessary argument from function call

Issue - State: closed - Opened by jakejh about 6 years ago
Labels: minor

#32 - Add elements to DESCRIPTION file

Issue - State: closed - Opened by jakejh about 6 years ago - 1 comment
Labels: minor

#31 - Shorten calls to foreach and data.table

Issue - State: closed - Opened by jakejh about 6 years ago
Labels: minor

#30 - Plot underlying sin curve in vignette time course

Issue - State: closed - Opened by ZackAttack614 about 6 years ago
Labels: enhancement, minor

#29 - Simplify calculation of nGroups

Issue - State: closed - Opened by jakejh about 6 years ago
Labels: minor

#28 - sd column should be specific to gaussian

Issue - State: closed - Opened by jakejh about 6 years ago
Labels: invalid

#27 - Incorrect check for single condition

Issue - State: closed - Opened by jakejh about 6 years ago
Labels: bug

#26 - dispersionFunc is created, but then not used (sampleDispersion is called instead)

Issue - State: closed - Opened by jakejh about 6 years ago
Labels: bug

#25 - Generalization

Pull Request - State: closed - Opened by ZackAttack614 about 6 years ago - 8 comments

#24 - Should Single-Condition Simulations Take a data.table Instead of list(data.table)?

Issue - State: closed - Opened by ZackAttack614 about 6 years ago - 2 comments
Labels: decision, minor

#23 - Didn't we decide to get rid of nSims?

Issue - State: closed - Opened by jakejh about 6 years ago - 1 comment
Labels: decision

#22 - Incorrect parameterization for negative binomial

Issue - State: closed - Opened by jakejh about 6 years ago - 2 comments
Labels: invalid

#21 - Easy way to generate data from a single condition

Issue - State: closed - Opened by jakejh about 6 years ago - 1 comment
Labels: enhancement

#20 - Minor renaming of function to generate counts

Issue - State: closed - Opened by jakejh about 6 years ago - 1 comment
Labels: decision

#19 - checkExprGroups is using data.table to modify exprGroups in-place

Issue - State: closed - Opened by jakejh about 6 years ago - 2 comments
Labels: invalid

#18 - Generalization

Pull Request - State: closed - Opened by ZackAttack614 about 6 years ago - 2 comments

#17 - Should getSimulatedGeneCounts Only Output Counts?

Issue - State: closed - Opened by ZackAttack614 about 6 years ago - 5 comments
Labels: decision

#16 - Nbinom test

Pull Request - State: closed - Opened by darwinyfu about 6 years ago

#15 - Adding options for simulating negative binomial read counts

Pull Request - State: closed - Opened by darwinyfu about 6 years ago

#14 - Simplify calculation of time-course

Issue - State: closed - Opened by jakejh about 6 years ago

#13 - Change Columns in exprGroups

Issue - State: closed - Opened by ZackAttack614 about 6 years ago
Labels: enhancement

#12 - Add option to simulate counts from a negative binomial distribution

Issue - State: closed - Opened by jakejh about 6 years ago
Labels: enhancement

#11 - Rename rhythmicGroups to exprGroups

Issue - State: closed - Opened by ZackAttack614 about 6 years ago
Labels: invalid

#10 - Arbitrary Rhythmic Function

Issue - State: closed - Opened by ZackAttack614 about 6 years ago
Labels: enhancement

#9 - Include Mean Phase in Simulated Expression

Issue - State: closed - Opened by ZackAttack614 about 6 years ago - 1 comment
Labels: duplicate

#8 - Generate rhythmicGroups from vectors of amplitudes and phases

Issue - State: closed - Opened by ZackAttack614 over 6 years ago - 1 comment
Labels: enhancement

#7 - Allow the manual setting of phase in rhythmicGroups

Issue - State: closed - Opened by ZackAttack614 over 6 years ago
Labels: enhancement

#6 - Allow for arbitrary number of DR genes & size of rhythmicGroups

Issue - State: closed - Opened by ZackAttack614 over 6 years ago
Labels: enhancement

#5 - Rename "geneId" to "gene"

Issue - State: closed - Opened by ZackAttack614 over 6 years ago
Labels: enhancement

#4 - Rename "rhyIndex" column to "groupIndex"

Issue - State: closed - Opened by ZackAttack614 over 6 years ago
Labels: enhancement

#3 - Add option to make condition a continuous variable

Issue - State: closed - Opened by ZackAttack614 over 6 years ago - 3 comments
Labels: enhancement, wontfix

#2 - Add option to make timepoints randomly spaced

Issue - State: closed - Opened by ZackAttack614 over 6 years ago
Labels: enhancement

#1 - Add option to specify fraction of DR genes allocated to each combination of parameters

Issue - State: closed - Opened by ZackAttack614 over 6 years ago
Labels: enhancement

GitHub / hugheylab/simphony issues and pull requests