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tolomatic-java

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Analyzed about 20 hours ago. based on code collected about 20 hours ago.

Commit Message	Contributor	Files Modified	Lines Added	Lines Removed	Code Location	Date
Jan 27, 2025 — Jan 27, 2026 Showing page 1 of 7 Search / Filter on:
adding abundanc X distance scripts and results	Rutger Vos	More...				almost 11 years ago
renaming...	Rutger Vos as rvosa	More...				almost 11 years ago
renaming...	Rutger Vos as rvosa	More...				almost 11 years ago
redid RyanCt jaccknifing	Rutger Vos as rvosa	More...				almost 11 years ago
redoing abundance by distance	Rutger Vos as rvosa	More...				almost 11 years ago
renaming...	Rutger Vos as rvosa	More...				almost 11 years ago
renamed Carla's trees to standardized names	Rutger Vos as rvosa	More...				almost 11 years ago
redid RyanCt jackknifing	Rutger Vos as rvosa	More...				almost 11 years ago
added comments	Rutger Vos as rvosa	More...				almost 11 years ago
adding comparative analysis of abundance over intraspecific distance	Rutger Vos as rvosa	More...				almost 11 years ago
pca script and visualization to show how pre and post separate	Rutger Vos as rvosa	More...				almost 11 years ago
'clade stats' selected terminal triplets to compute summary statistics over. visualization (*_n3.svg, PCA.pdf) shows that post is more stemmy	Rutger Vos as rvosa	More...				almost 11 years ago
adding script to apply QIIME taxonomy (rightmost column) to trees leaf-labeled with leftmost column (OTU IDs)	Rutger Vos as rvosa	More...				almost 11 years ago
adding script to draw a set of triplet trees superimposed on each other	Rutger Vos as rvosa	More...				almost 11 years ago
adding first stab at correlating abundance with intraspecific variation	Rutger Vos as rvosa	More...				almost 11 years ago
incomplete RyanCt results	Rutger Vos as rvosa	More...				almost 11 years ago
adding local BLAST database of all reads - using this only for fast lookup of records	Rutger Vos as rvosa	More...				almost 11 years ago
adding DESeq2-normalized OTU table	Rutger Vos as rvosa	More...				almost 11 years ago
adding CSS-normalized OTU table	Rutger Vos as rvosa	More...				almost 11 years ago
adding original OTU table translated to biom (JSON) format	Rutger Vos as rvosa	More...				almost 11 years ago
adding log-transformed, normalized abundances. homegrown method - those in QIIME are probably better	Rutger Vos as rvosa	More...				almost 11 years ago
re-ran clade stats	Rutger Vos	More...				almost 11 years ago
now passes the tree object into the template, so we can be flexible with any additional clade stats	Rutger Vos as rvosa	More...				almost 11 years ago
removing too-generic histograms script	Rutger Vos as rvosa	More...				almost 11 years ago
adding script to plot Colless Imbalance histograms	Rutger Vos as rvosa	More...				almost 11 years ago
adding script to plot F&S stemminess	Rutger Vos as rvosa	More...				almost 11 years ago
adding script to plot AVTD histograms	Rutger Vos as rvosa	More...				almost 11 years ago
adding scripts and logs for clade (N=XXX) statistics	Rutger Vos as rvosa	More...				almost 11 years ago
Merge branch 'master' of github.com:naturalis/tolomatic-java	Rutger Vos as rvosa	More...				almost 11 years ago
different avtd-ish algorithm	Rutger Vos	More...				almost 11 years ago

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