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

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.

Author
Elsa Bernard, Laurent Jacob, Julien Mairal and Jean-Philippe Vert
Date of publication
None
Maintainer
Elsa Bernard <elsa.bernard@mines-paristech.fr>
License
GPL-3
Version
1.12.0
URLs

View on Bioconductor

Man pages

flipflop
Estimate isoform compositions and abundances

Files in this package

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