peco - vignette edits

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Published by jhsiao999 over 6 years ago

peco - add cell cycle gene list

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Published by jhsiao999 over 6 years ago

peco - minor bug fixes + vignette

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Published by jhsiao999 over 6 years ago

peco - use SingleCellExperiment S4 object as input/output to main functions

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Published by jhsiao999 over 6 years ago

peco - bump to v0.99.4

• passed Travis CI and Circle I checks

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Published by jhsiao999 almost 7 years ago

peco - use SingleCellExperiment class

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Published by jhsiao999 almost 7 years ago

peco - tell Travis CI to not test in R old release

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Published by jhsiao999 almost 7 years ago

peco - R dependency changed to 3.6

also fixed errors and warnings from R CMD Check and R CMD BiocCheck

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Published by jhsiao999 almost 7 years ago

peco - submitted to Bioconductor

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Published by jhsiao999 almost 7 years ago

peco - minor fixes

• Add grids argument to cycle_npreg_outsample() function

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Published by jhsiao999 almost 7 years ago

peco - minor fixes

• DESCRIPTION: Update date and version` in

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Published by jhsiao999 over 7 years ago

peco - minor fixes and improvements

notes (Peter's comments before v0.6.0)

• Please fix: I don't understand the description of the esetfinalsub data set. What are "theta" and "exprs(est_final)"?

  • fixed

• Please fix: The "fit" data set should be a single object; currently it loads two objects, "fitpredict" and "fittrain". Maybe define a list with two elements. Also, I suggest using a more descriptive name.

  • made into two separate data objects

• Please fix: Why do "fitbspline" and "fitloess" return a list with only one element? You don't need the list.

  • added pve calculations. so now a list of two vectors.

• Please fix: some undocumented arguments that should be added to the roxygen2 docs:

  • Undocumented arguments in cyclenpreginsample: ‘...’
  • Undocumented arguments in cyclenpregloglik: grids, method.type, method.grid ‘...’
  • Undocumented arguments in cyclenpregmstep: method.trend, polyorder, ncores, ‘...’
  • Undocumented arguments in cyclenpregoutsample: ‘...’
  • Undocumented arguments in initialize_grids: ‘...’
  • Undocumented arguments in run_seurat: s.genes, g2m.genes, n.bin, seed.use, random.seed
  • ALL FIXED!

• Please fix: Add an inst/CITATION file; see github.com/stephenslab/mixsqp for an example.

  • fixed!

• Suggestion: In the file circlenpreg.R, the functions are "cyclenpreg_*". Maybe hange the name of the file to be consistent.

  • changed to cycle_npreg.R!

• Suggestion: Explain in "Description" field of DESCRIPTION file why it is called "peco". (And in README!)

  • PrEdicting Cell cycle prOgression in a continuum using scRNA-seq data

• Suggestion: If reasonable to do so, reduce size of data sets in "data" folder in order to reduce installation time from GitHub.

• Suggestion: Create a "release" on GitHub. (I can show you how.)

  • First realease 0.6.1

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Published by jhsiao999 over 7 years ago

peco - first release

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Published by jhsiao999 over 7 years ago