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julianspagnuolo / fackit Goto Github PK

FACkit is a complete R toolkit providing transformation, data-exploration, dimensional-reduction and clustering methods tailored to semi-automated analysis of FACS data

License: GNU General Public License v3.0

R 97.09% C++ 2.91%

bioinformatics flow-cytometry-analysis bioconductor

fackit's Introduction

FACkit

Installation

You can install FACkit from github with:

# install.packages("devtools")
devtools::install_github("JulianSpagnuolo/FACkit")

Citation

It is requested that users publishing or presenting work that utilise this package in part or wholey cite it using

#> 
#> To cite package 'FACkit' in publications use:
#> 
#>   Julian Spagnuolo (2017). FACkit: FACS Analysis Tool Kit. R
#>   package version 0.1.3.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {FACkit: FACS Analysis Tool Kit},
#>     author = {Julian Spagnuolo},
#>     year = {2017},
#>     note = {R package version 0.1.3},
#>   }
#> 
#> ATTENTION: This citation information has been auto-generated from
#> the package DESCRIPTION file and may need manual editing, see
#> 'help("citation")'.

fackit's People

Contributors

Forkers

giannimonaco marcin331

fackit's Issues

facsnorm

Make option to choose:

arcsin transformation
logical transformation (with log transformation) i.e. add min(marker)+1 to all values and log transform (try with and without centre scaling using cutoffs (or log of sign(diff() for negative cutoff values))

Cutoffs Accessor Function

Write function to retrieve chosen cutoffs from cutfind2 results and pass them to facsnorm

Cutoffs Plot Function

Write new function to plot models and cutoffs determined by the cutfind2 function

MEM

Bugs in MEM function when using statistic="mode" and ref.pops are not defined. (Also occurs if ref.pops are defined)....

"the condition has length > 1 and only the first element will be used"
"longer object length is not a multiple of shorter object length"

Fix short-circuiting in cell state network graph

Find better method to model the main clusters in Diffusion Space as a graph network and maintain branches to prevent short-circuits created by 2 cell-states stemming off the same root node (but are in different branches).

cutfind error code 13 at estep

Cutfind auto model optimisation

optimise the model choice.
if difference in BIC/AIC is less than some factor choose the simpler model (i.e one with fewer components)

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