v.2.2.1

Code

2.2.1 version

• Add repSave() for saving repertoires or a lists of repertoires to disk.
• Add repLoad() - a general function for loading data frames from various sources (text files, gzip files, folders, mixed list of files and folders).
• Add parse.tcr function for parsing tcR data frames saved with repSave.
• Add a boxplot for intersections.
• Add matrixSubgroups.
• Add a metric of differences of intersections among a number of groups. link1 - function permutDistTest.
• Z-scores for overlaps.

Other

2.2.1 version

• Add rhesus monkey trbv and trbj.

v2.1.1

fix read.table() skipping many rows

v2.1

Changes from v2.0 to v2.1 have been lost in a mysterious chain of events...

v2.0

Code

2.0 version

• Now tcR operates on default cloneset data frames with fixed columns. Input functions are changed to match this.
• Rename *.segments to *.gene columns.
• Rename freq.segments to geneUsage and refactor arguments, esp. .alphabet = HUMAN_TRBV.
• Merge freq.segments and freq.segments.2D to the one function geneUsage.
• Rename mitcr.stats to cloneset.stats.
• Rename lib.mitcr.stats to repseq.stats.
• Rename tcR::intersect to intersectClonesets to avoid collisions.
• Replace vis.*.usage with general function vis.gene.usage.
• Add general function for computing the repertoire overlap repOverlap.
• Add general function for computing the repertoire diversity repDiversity.
• Rename "Barcode." columns to "Umi.".

Vignette

2.0 version

• Rewrite vignette using Rmd and knitr.

Other

2.0 version

• Rename ___ALPHABET to just **.
• Rewrite reports.
• Update the website with the new vignette, examples of general functions, versions.
• Upload 2.0 to CRAN.

v1.3.1

Just for getting the DOI

v1.3

Code

• Add generic parser for table files.
  • Add parser for MiTCR w/o barcodes.
  • Add parser for MiTCR w/ barcodes.
  • Add parser for MiGEC.
• Refactor set.group.vector so it doesn't use shared repertoires as an input.
• Refactor repertoire data frames, change column names to more general and oth.
• Add function group.clonotypes for merging together clonotypes by sequence and gene segments.

Documentation

• Add docs for new parsers.
• Add documentation for mutation.network.
• Probably rename repertoire graphs to something a bit more clear like "mutation graph" => renamed to "mutation network".
• Add docs to mutated.neighbors.

Vignette

• Fix abstract.
• Add docs about new data frames and parsers.
• Add more clear Quick Start / examples.
• Add mutation networks examples and functions' descriptions.
• Add logo function description.
• Add clonal space homeostasis examples and function description.
• Add visualisations for logo, clonal space homeostasis, clonal dynamics.
• Update the vignette at tcR site.

Other

• Release 1.3 version - here and on CRAN.
• Rename segments data to genesegments to avoid conflicts.

v1.2

update documentation

v1.0

no message