flipflop: Fast lasso-based isoform prediction as a flow problem
Version 1.14.1

Flipflop discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. It takes an alignment file in SAM format as input. It can also discover transcripts from several samples simultaneously, increasing statistical power.

Browse man pages Browse package API and functions Browse package files

AuthorElsa Bernard, Laurent Jacob, Julien Mairal and Jean-Philippe Vert
Bioconductor views AlternativeSplicing RNASeq RNASeqData Regression
Date of publicationNone
MaintainerElsa Bernard <elsa.bernard@mines-paristech.fr>
LicenseGPL-3
Version1.14.1
URL http://cbio.ensmp.fr/flipflop
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("flipflop")

Getting started

Man pages

flipflop: Estimate isoform compositions and abundances

Functions

R_SWIG_addCallbackFunctionStack Source code
R_SWIG_getCallbackFunctionStack Source code
SWIG_createNewRef Source code
WrapperFlipFlop Source code
WriteOutput Source code
assert Source code
bin.inside Source code
bins_paired Source code
calculate.cost Source code
coerceIfNotSubclass Source code
collect_path_grouplasso Source code
defineEnumeration Source code
duality_gap_poisson Source code
duality_gap_poisson_graph Source code
enumFromInteger Source code
enumToInteger Source code
find.prefix Source code
findpas Source code
findtss Source code
firstexon Source code
flipflop Man page Source code
graph_paired Source code
graph_single Source code
grouplassoPoisson Source code
lastexon Source code
loss.ll Source code
max_lambda Source code
modelselection Source code
processsam Source code
quickmatch Source code
refitPoisson Source code
refitSamples Source code
regularization_path Source code
regularization_path_grouplasso_dich Source code
spams_flipflop.evalPathCoding Source code
spams_flipflop.fistaFlat Source code
spams_flipflop.multLeftDiag Source code
spams_flipflop.sepCostsPathCoding Source code
spams_flipflop.solverPoisson Source code
spams_flipflop.solverPoissonFull Source code
startstop Source code
startstop_paired Source code
tic Source code
toc Source code
write.exons Source code
write.exons.short Source code
write.transcript Source code
write.transcript.short Source code

Files

DESCRIPTION
NAMESPACE
R
R/ModelSelection.R
R/PoissonLoss.R
R/WrapperFlipFlop.R
R/WriteOutput.R
R/bins_paired.R
R/collect_path_grouplasso.R
R/duality_gap_poisson.R
R/duality_gap_poisson_graph.R
R/ff_spams.R
R/flipflop.R
R/graph_paired.R
R/graph_single.R
R/grouplassoPoisson.R
R/max_lambda.R
R/processsam.R
R/refitPoisson.R
R/refitSamples.R
R/regularization_path.R
R/regularization_path_grouplasso_dich.R
R/spamsff.R
R/tictoc.R
R/utils.R
build
build/vignette.rds
inst
inst/CITATION
inst/COPYING
inst/NEWS
inst/doc
inst/doc/flipflop.R
inst/doc/flipflop.Rnw
inst/doc/flipflop.pdf
inst/extdata
inst/extdata/flipflop.Rex
inst/extdata/vignette-annot.bed.txt
inst/extdata/vignette-sam.txt
inst/scripts
inst/scripts/generateManPages.R
man
man/flipflop.Rd
src
src/FileSplitter.cpp
src/FileSplitter.h
src/Makevars
src/R_init_flipflop.c
src/R_init_flipflop.h
src/Rinterface.h
src/align.cpp
src/align.h
src/auxiliaryio.cpp
src/auxiliaryio.h
src/bedio.cpp
src/bedio.h
src/common.cpp
src/common.h
src/commontype.h
src/cvganalysis.cpp
src/cvganalysis.h
src/ffProcesssam.cpp
src/instanceio.cpp
src/instanceio.h
src/parseopt.cpp
src/parseopt.h
src/rangeset.cpp
src/rangeset.h
src/readgroup.cpp
src/readgroup.h
src/samio.cpp
src/samio.h
src/samples.cpp
src/samples.h
src/spams
src/spams.cpp
src/spams.h
src/spams/dags
src/spams/dags/dag.h
src/spams/decomp
src/spams/decomp/decomp.h
src/spams/linalg
src/spams/linalg/cblas_alt_template.h
src/spams/linalg/cblas_defvar.h
src/spams/linalg/cblas_template.h
src/spams/linalg/linalg.h
src/spams/linalg/list.h
src/spams/linalg/mexutils.h
src/spams/linalg/misc.h
src/spams/linalg/utils.h
src/spams/prox
src/spams/prox/fista.h
src/spams/prox/project.h
src/structdef.cpp
src/structdef.h
src/utils.h
vignettes
vignettes/biblio.bib
vignettes/flipflop.Rnw
flipflop documentation built on May 20, 2017, 10:32 p.m.