NEWS.md

In LieberInstitute/jaffelab: Commonly used functions by the Jaffe lab

jaffelab 0.99.34

• Updated internal code in the package to make it compliant with BiocCheck.

jaffelab 0.99.33

• merge_rse_metrics() can now also handle ERCCsumLogErr. Note that its an approximation given properties of logarithms. To compute the actual correct values, you would need access to the original output ERCC quantification output files.

jaffelab 0.99.32

• Added the skipLines argument to junctionCount to resolve https://github.com/LieberInstitute/jaffelab/issues/8.

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 ofcleaningY(). This is after Stephen Semick and Emily Burke reported issues with the function.

jaffelab 0.99.13

SIGNIFICANT USER-VISIBLE CHANGES

• Moved coverage_bwtool() to the recount.bwtool package.

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().

LieberInstitute/jaffelab documentation built on April 1, 2024, 7:26 a.m.