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jaffelab 0.99.30

  • cleaningY() now supports NAs in the input y.

jaffelab 0.99.29

  • Added the googledrive_csv() function for uploading CSV files to Google Drive. It used to be internal code of lab_presenters() but could be more useful outside of it.

jaffelab 0.99.28

  • Added the lab_presenters() function for randomizing lab presenters. Could also be used for randomizing the lab snacks rotation.

jaffelab 0.99.27

  • Added a NEWS.md file to track changes to the package, thus replacing the existing NEWS file.
  • Created a pkgdown::build_site() version for the documentation of the package.

jaffelab 0.99.26

NEW FEATURES

  • Added examples to agePlotter(), cleaningY(), getR2(), edge.pvalue() and noted that junctionCount() is missing a full example.

jaffelab 0.99.25

NEW FEATURES

  • Added the functions n_max() and n_min() which return the top n maximum or minimum values of a vector.

jaffelab 0.99.23

NEW FEATURES

  • Added the function merge_rse_metrics() that merges some of the sample metadata metrics for samples that were sequenced in more than one lane. Useful for the RangedSummarizedExperiment objects we typically produce for RNA-seq experiments at the Jaffe lab.

jaffelab 0.99.22

NEW FEATURES

  • Added the granges_to_ucsc() function, which is the reverse of ucsc_to_granges().

jaffelab 0.99.21

NEW FEATURES

  • Added the function corner() which takes head of rows and columns of objects

jaffelab 0.99.20

SIGNIFICANT USER-VISIBLE CHANGES

  • agePlotter(): changed how the X-axis ticks and range are made for the prenatal samples.

jaffelab 0.99.19

NEW FEATURES

  • Introduced the ucsc_to_granges() function that converts a character vector of coordinates from the UCSC genome browser to a GRanges object.

jaffelab 0.99.18

SIGNIFICANT USER-VISIBLE CHANGES

  • agePlotter() is now more flexible and can handle up a vector of pointColor and lineColor. Also, the breaks are now flexible and support more scenarios (you need at least 3 groups).

jaffelab 0.99.16

SIGNIFICANT USER-VISIBLE CHANGES

  • GitHub repo is now public.

jaffelab 0.99.15

NEW FEATURES

  • Added the function expression_cutoff() which finds suggested expression cutoffs for an RPKM matrix.

jaffelab 0.99.14

BUG FIXES

  • Corrected the documentation of cleaningY(). This is after Stephen Semick and Emily Burke reported issues with the function.

jaffelab 0.99.13

SIGNIFICANT USER-VISIBLE CHANGES

jaffelab 0.99.12

NEW FEATURES

  • Added the function coverage_bwtool() for computing coverage matrices using bwtool for a user-specified list of bigWig files and a user-specified phenotype table. It's heavily based on recount.bwtool

jaffelab 0.99.11

SIGNIFICANT USER-VISIBLE CHANGES

  • junctionCount() uses check.names = FALSE when calling DataFrame(). Related to a bug Badoi Phan reported.

jaffelab 0.99.8

BUG FIXES

  • Added code by Emily Burke that makes junctionCount() work for single-end libraries. Still need to trace why ? are being added as the strand.

jaffelab 0.99.10

NEW FEATURES

  • Added the getT() function.

jaffelab 0.99.7

NEW FEATURES

  • Added agePlotter() -- missing examples and tests

jaffelab 0.99.6

NEW FEATURES

  • Added junctionCount() -- missing examples and tests

jaffelab 0.99.5

NEW FEATURES

  • Added getR2() -- missing examples and tests

jaffelab 0.99.4

NEW FEATURES

  • Added cleaningY() -- missing examples and tests

jaffelab 0.99.3

NEW FEATURES

  • Added getOR()

jaffelab 0.99.2

SIGNIFICANT USER-VISIBLE CHANGES

  • Dropped splitit() since it's available in rafalib.
  • Now depending on rafalib making those functions available to the user.

jaffelab 0.99.0

NEW FEATURES

  • Added ss() as a wrapper for string split() and sapply().
  • Added splitit() and split0() that splits a vector into a list and return the integer indexes of the elements.
  • Added getPcaVars() which computes the percent of variance explained for the principal components of prcomp object.
  • Added getF().