Julia interface to ViennaRNA for RNA structure prediction and analysis
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Merged pull requests:
Published by github-actions[bot] over 1 year ago
Closed issues:
plot_coords("()")
(#13)Merged pull requests:
Published by github-actions[bot] over 1 year ago
Merged pull requests:
Published by github-actions[bot] over 1 year ago
There is a new way of changing energy parameters that more closely mirrors the ViennaRNA API and allows for higher performance. Now energy parameters are changed by calling e.g. ViennaRNA.params_load(:RNA_Turner1999)
or ViennaRNA.params_load_RNA_Turner1999()
. All FoldCompound
s constructed afterwards will then use these parameters. The old way of setting the parameters via a keyword argument in the constructor FoldCompound(...; params=:RNA_Turner1999)
does not work anymore.
Closed issues:
Published by github-actions[bot] almost 2 years ago
new functions
mfe_window
mfe_window_channel
ViennaRNA.init_rand_seed
set options
with Symbols instead of Integers in various functions
FoldCompound
max_bp_span
and window_size
sample_structures
is the new name for pbacktrack
(the same as in RNAstructure.jl and LinearFold.jl)
plot_coords
defaults to the :puzzler
plot type (like in the ViennaRNA C library)
Closed issues:
Merged pull requests:
Published by github-actions[bot] about 2 years ago
Closed issues:
Published by github-actions[bot] over 2 years ago
Published by github-actions[bot] over 2 years ago
Published by github-actions[bot] over 2 years ago
Published by github-actions[bot] over 2 years ago
Published by github-actions[bot] over 2 years ago
Published by github-actions[bot] over 2 years ago
Published by github-actions[bot] over 2 years ago
Published by github-actions[bot] over 2 years ago
Changes since v0.5.0:
plot_structure
and plot_structure_makie
functions to draw secondary structures with Cairoheat_capacity
functionplot_coords
defaults to the 'simple' layout algorithmPublished by github-actions[bot] over 2 years ago
Closed issues:
Merged pull requests:
Published by github-actions[bot] over 2 years ago
bpp
now returns a symmetric matrix of basepair probabilitiesprob_of_basepairs
function that calculates the probability of every basepair or unpaired base for a (sequence, structure) pairplot_structure
function that implements a simple form of secondary structure plotting with base coloring (see issue #3)Published by github-actions[bot] over 2 years ago
Published by github-actions[bot] over 2 years ago
FoldCompound
uniq_ML
argument to FoldCompound
is now of type Bool
Published by github-actions[bot] over 2 years ago
pbacktrack
, subopt
, subopt_zuker
Closed issues:
Published by marcom over 2 years ago
ViennaRNA_jll v2.5.0
Clang.jl
instead of CBinding
(CBinding required C standard header files installed at runtime)Fixes #1