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BTR (version 1.2.4)

Training and Analysing Asynchronous Boolean Models

Description

Tools for inferring asynchronous Boolean models from single-cell expression data.

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Version

Install

install.packages('BTR')

Monthly Downloads

22

Version

1.2.4

License

GPL-3

Maintainer

Chee Yee Lim

Last Published

September 13th, 2016

Functions in BTR (1.2.4)

BTR

BTR: A package for studying asynchronous Boolean models
bon_istate

Initial state from Bonzanni et al.
calc_roc

Calculate precision, recall, f-score, accuracy and specificity
compress_bmodel

Compress BoolModel
bm_to_amat

Convert BoolModel into adjacency matrix
filter_dflist

Filter columns of df in a list
gen_one_rmodel

Generate a random Boolean model
decompress_bmodel

Decompress BoolModel
df_to_bm

Convert a data frame into BoolModel object
decreate_boolmodel

Decreate Boolean model
emodel1

Example Boolean Model used in the vignette
emodel3

Example Boolean Model used in the vignette
emodel2

Example Boolean Model used in the vignette
eval_bool

Evaluating Boolean rules
extract_term

Extract Boolean terms
get_encodings

Get corresponding encodings for compression or decompression.
grow_bmodel

Add extra genes to a Boolean model
initialise_data

Initialise data
initialise_raw_data

Initialise raw data
gen_singlerule

Generate random act and inh rule for a single gene
gen_two_rmodel_dag

Generate two random DAG Boolean models with a specified number of steps apart
initialise_model

Initialise model
gen_two_rmodel

Generate two random Boolean models with a specified number of steps apart
minmod_internal

Inner function of minimal modification of whole Boolean model
outgraph_model

Output a Boolean Model into Cytoscape & Gephi readable format
minmod_model

Minimal modification of whole Boolean model
match_term

Check for matching terms
man_dist

Calculates pairwise Manhattan distances between two matrices
model_train

Training Model
model_setdiff

Find the set difference between two Boolean models
model_consensus

Intersection of genes
model_dist

Calculate distance between Boolean models
outgenysis_model

Output a Boolean Model into Genysis readable format
rcpp_validate

Calculating validation scores between two adjacency matrices
plotBM

Plot Boolean Model
simulate_model

Simulating Boolean model
outstate_graph

Generate state transition graph
vcat

Verbose cat
printBM

Print Boolean Model
which.random.min

Pick a random minimum value
unique_raw_data

Remove raw data duplicated wrt to the model state
validate_adjmat

Calculate true positive, true negative, false positive and false negative
writeBM

Write Boolean Model
krum_istate

Initial state from Krumsiek et al.
krum_bmodel

Myeloid Boolean Model from Krumsiek et al.
wilson_raw_data

Raw single cell qRT-PCR expression data from Wilson et al.
amat_to_bm

Convert adjacency matrix into BoolModel object
wilson_raw_rnaseq

Raw single cell RNAseq expression data from Wilson et al.
bon_bmodel

HSC Boolean Model from Bonzanni et al.
rcpp_simulate

Simulate a Boolean model.
bm_to_df

Convert BoolModel object into BoolNet readable data frame
check_and

Check if containing AND terms
calc_mscore

Calculating Boolean model score wrt to a dataset