drisso/archive-zinbwave issues and pull requests

#47 - Bug: installation fails on Windows 10/R 3.4.3

Issue - State: closed - Opened by chiffa over 6 years ago - 2 comments

#46 - Error: 'vmmin' is not finite

Issue - State: open - Opened by davismcc about 7 years ago - 4 comments

#45 - Add argument to zinbwave() to use another assay(), currently only first is used

Issue - State: open - Opened by drisso over 7 years ago

#44 - zinbwave() error: initial value in 'vmmin' is not finite

Issue - State: closed - Opened by drisso over 7 years ago - 4 comments
Labels: bug

#43 - avoid inf in log lik

Pull Request - State: closed - Opened by fperraudeau over 7 years ago - 1 comment
Labels: enhancement

#42 - Vignette dependence on biomart

Issue - State: open - Opened by drisso over 7 years ago

#41 - Adding a variation metric to getW output

Issue - State: open - Opened by nachocab over 7 years ago - 1 comment

#41 - Adding a variation metric to getW output

Issue - State: open - Opened by nachocab over 7 years ago - 1 comment

#40 - Very slow when using BiocParallel

Issue - State: closed - Opened by drisso over 7 years ago - 3 comments

#39 - Allow user to specify NULL X and/or V?

Issue - State: open - Opened by drisso over 7 years ago
Labels: low priority

#39 - Allow user to specify NULL X and/or V?

Issue - State: open - Opened by drisso over 7 years ago
Labels: low priority

#38 - Bioconductor revision

Issue - State: closed - Opened by drisso over 7 years ago - 2 comments

#37 - Add sticker to BiocStickers repo

Issue - State: closed - Opened by jorainer over 7 years ago - 2 comments

#37 - Add sticker to BiocStickers repo

Issue - State: closed - Opened by jorainer over 7 years ago - 2 comments

#36 - Check that input matrix is whole numbers

Issue - State: closed - Opened by drisso over 7 years ago - 2 comments
Labels: high priority

#35 - Error in qr.default(t(V)) : NA/NaN/Inf in foreign function call (arg 1)

Issue - State: closed - Opened by nachocab over 7 years ago - 3 comments

#35 - Error in qr.default(t(V)) : NA/NaN/Inf in foreign function call (arg 1)

Issue - State: closed - Opened by nachocab over 7 years ago - 3 comments

#34 - Use just for normalisation?

Issue - State: closed - Opened by JohnReid over 7 years ago - 12 comments

#33 - get_alpha methods

Issue - State: closed - Opened by drisso over 7 years ago - 1 comment

#33 - get_alpha methods

Issue - State: closed - Opened by drisso over 7 years ago - 1 comment

#32 - Clustering after model fitting

Issue - State: closed - Opened by nachocab over 7 years ago - 2 comments

#32 - Clustering after model fitting

Issue - State: closed - Opened by nachocab over 7 years ago - 2 comments

#31 - wrong dimensions in zinbFit()

Issue - State: closed - Opened by drisso over 7 years ago

#31 - wrong dimensions in zinbFit()

Issue - State: closed - Opened by drisso over 7 years ago

#30 - Error when fitting with zero fraction = 75%

Issue - State: closed - Opened by fperraudeau almost 8 years ago - 4 comments
Labels: bug

#30 - Error when fitting with zero fraction = 75%

Issue - State: closed - Opened by fperraudeau almost 8 years ago - 4 comments
Labels: bug

#29 - Faster svd

Issue - State: closed - Opened by drisso about 8 years ago - 2 comments
Labels: enhancement

#29 - Faster svd

Issue - State: closed - Opened by drisso about 8 years ago - 2 comments
Labels: enhancement

#28 - Possible conflict between branches

Issue - State: closed - Opened by jpvert about 8 years ago - 1 comment

#28 - Possible conflict between branches

Issue - State: closed - Opened by jpvert about 8 years ago - 1 comment

#27 - the world of the epsilons

Issue - State: closed - Opened by fperraudeau about 8 years ago - 1 comment
Labels: documentation

#27 - the world of the epsilons

Issue - State: closed - Opened by fperraudeau about 8 years ago - 1 comment
Labels: documentation

#26 - consistency in dimensions between Y and getMu(), getPi()

Issue - State: closed - Opened by fperraudeau about 8 years ago - 1 comment
Labels: enhancement

#26 - consistency in dimensions between Y and getMu(), getPi()

Issue - State: closed - Opened by fperraudeau about 8 years ago - 1 comment
Labels: enhancement

#25 - loading message

Issue - State: open - Opened by fperraudeau about 8 years ago - 7 comments
Labels: bug

#25 - loading message

Issue - State: open - Opened by fperraudeau about 8 years ago - 7 comments
Labels: bug

#24 - Passing offsets to zinbFit

Issue - State: open - Opened by drisso about 8 years ago
Labels: enhancement, low priority

#24 - Passing offsets to zinbFit

Issue - State: open - Opened by drisso about 8 years ago
Labels: enhancement, low priority

#23 - ZinbSim should simulate a matrix with genes in rows

Issue - State: closed - Opened by drisso about 8 years ago
Labels: high priority

#23 - ZinbSim should simulate a matrix with genes in rows

Issue - State: closed - Opened by drisso about 8 years ago
Labels: high priority

#22 - Updated the vignette with missing details on gradient computations

Pull Request - State: closed - Opened by jpvert about 8 years ago

#22 - Updated the vignette with missing details on gradient computations

Pull Request - State: closed - Opened by jpvert about 8 years ago

#21 - Bug in getPi

Issue - State: closed - Opened by drisso over 8 years ago
Labels: bug

#21 - Bug in getPi

Issue - State: closed - Opened by drisso over 8 years ago
Labels: bug

#20 - In model2.pdf penalties should be vectors not scalars

Issue - State: closed - Opened by drisso over 8 years ago - 1 comment
Labels: documentation

#20 - In model2.pdf penalties should be vectors not scalars

Issue - State: closed - Opened by drisso over 8 years ago - 1 comment
Labels: documentation

#19 - Fix documentation of W matrix

Issue - State: closed - Opened by drisso over 8 years ago
Labels: documentation

#19 - Fix documentation of W matrix

Issue - State: closed - Opened by drisso over 8 years ago
Labels: documentation

#18 - zinbInitialize() needs constraint for intercept

Issue - State: closed - Opened by drisso over 8 years ago

#18 - zinbInitialize() needs constraint for intercept

Issue - State: closed - Opened by drisso over 8 years ago

#17 - make zinbInitialize() parallel

Issue - State: closed - Opened by drisso over 8 years ago

#17 - make zinbInitialize() parallel

Issue - State: closed - Opened by drisso over 8 years ago

#16 - glmnet() does not work when only 1 or 0 in one category

Issue - State: closed - Opened by drisso over 8 years ago - 1 comment

#16 - glmnet() does not work when only 1 or 0 in one category

Issue - State: closed - Opened by drisso over 8 years ago - 1 comment

#15 - Implement special case ridge regression for pi (e.g., only one covariate)

Issue - State: closed - Opened by drisso over 8 years ago - 2 comments

#15 - Implement special case ridge regression for pi (e.g., only one covariate)

Issue - State: closed - Opened by drisso over 8 years ago - 2 comments

#14 - Create intercept_X and intercept_V slot + methods

Issue - State: closed - Opened by drisso over 8 years ago

#14 - Create intercept_X and intercept_V slot + methods

Issue - State: closed - Opened by drisso over 8 years ago

#13 - Check penalization terms in zinbFit

Issue - State: closed - Opened by drisso over 8 years ago

#13 - Check penalization terms in zinbFit

Issue - State: closed - Opened by drisso over 8 years ago

#12 - Arguments to be passed to zinbFit

Issue - State: closed - Opened by drisso over 8 years ago - 3 comments
Labels: enhancement

#12 - Arguments to be passed to zinbFit

Issue - State: closed - Opened by drisso over 8 years ago - 3 comments
Labels: enhancement

#11 - Implement zinbFit method for summarizedExperiment

Issue - State: closed - Opened by drisso over 8 years ago - 1 comment
Labels: enhancement

#11 - Implement zinbFit method for summarizedExperiment

Issue - State: closed - Opened by drisso over 8 years ago - 1 comment
Labels: enhancement

#10 - penalty_alpha_mu must be scalar?

Issue - State: closed - Opened by drisso over 8 years ago - 3 comments

#10 - penalty_alpha_mu must be scalar?

Issue - State: closed - Opened by drisso over 8 years ago - 3 comments

#9 - Turn zinbFit function into method

Issue - State: closed - Opened by drisso over 8 years ago - 1 comment

#9 - Turn zinbFit function into method

Issue - State: closed - Opened by drisso over 8 years ago - 1 comment

#8 - consider importing nSamples and nFeatures instead of using getN and getJ

Issue - State: closed - Opened by drisso over 8 years ago - 3 comments
Labels: question

#8 - consider importing nSamples and nFeatures instead of using getN and getJ

Issue - State: closed - Opened by drisso over 8 years ago - 3 comments
Labels: question

#7 - coding style!

Issue - State: closed - Opened by drisso over 8 years ago - 3 comments

#7 - coding style!

Issue - State: closed - Opened by drisso over 8 years ago - 3 comments

#6 - S4 class and main functions

Issue - State: closed - Opened by drisso over 8 years ago

#6 - S4 class and main functions

Issue - State: closed - Opened by drisso over 8 years ago

#5 - Improve initialization step

Issue - State: closed - Opened by drisso over 8 years ago

#5 - Improve initialization step

Issue - State: closed - Opened by drisso over 8 years ago

#4 - Preprocess the input with the right offsets

Issue - State: closed - Opened by drisso over 8 years ago - 2 comments

#4 - Preprocess the input with the right offsets

Issue - State: closed - Opened by drisso over 8 years ago - 2 comments

#3 - Simplify notation to remove U gamma

Issue - State: closed - Opened by drisso over 8 years ago

#3 - Simplify notation to remove U gamma

Issue - State: closed - Opened by drisso over 8 years ago

#2 - Phi optimization as a separate step

Issue - State: closed - Opened by drisso over 8 years ago - 1 comment

#2 - Phi optimization as a separate step

Issue - State: closed - Opened by drisso over 8 years ago - 1 comment

#1 - Likelihood does not always increase

Issue - State: closed - Opened by jpvert over 8 years ago - 1 comment

#1 - Likelihood does not always increase

Issue - State: closed - Opened by jpvert over 8 years ago - 1 comment

GitHub / drisso/archive-zinbwave issues and pull requests