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Basepair probs #217

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Basepair probs #217

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@Fulanko
PredictionTrackerBasePairProb layout
c55bac1
@Fulanko
added base-pair probability recursion
b249550
@Fulanko
updated PredictionTrackerBasePairProb + added dot plot (probabilities…
7d9720a 
… still incorrect)
@Fulanko
fixed overallHybridizationZ
c44bdee
@Fulanko
code cleanup
8e496f7
@Fulanko
fixed probabilities of > 1
2d9d5f7
@Fulanko
various fixes and cleanup in PredictionTrackerBasePairProb
79d6ff8
@Fulanko
added versions to postscript comment
8e061e1
@Fulanko
added code for seedbased base-pair probs (Not working correctly)
306f254
@Fulanko
Merge branch 'dev' into basepair-probs
17f4bcc
@Fulanko
rebase fixes
83e2dd8
@Fulanko
fixed some missing changes
a2c4d75
@Fulanko
Merge branch 'dev' into basepair-probs
42676bf 
# Conflicts:
#	src/IntaRNA/PredictorMfeEnsSeedOnly.cpp
@Fulanko
added test for Zall
b6e06e0
@Fulanko
refactored predictionTrackerBasePairProb
3205b3e
@Fulanko
changed getZ -> getHybridZ + added default argument to reportZ
3158bf3
@Fulanko
fixed basepairProb tracker bugs + added test
019422f
@Fulanko
refactor
b7587f7
@Fulanko
added script for basepair prob dot plots
88841c0
@Fulanko
fixed reversed sequence in dotplot
81c2116
@Fulanko
added python script to compute concentrations of homo/hetero dimers
e3f01f3
@Fulanko
input validation
f96bab0
@Fulanko
outer loop changes
f2fbff6
@Fulanko
Merge branch 'dev' into basepair-probs
6fd8c3e
@Fulanko
renamed test + changed IntaRNA_precisionEpsilon
40e2f36
@Fulanko
renamed test
c956c68
@Fulanko
changed dotplot template to inline string
7ae5cf6
@Fulanko
intaRNAtube.py refactoring
c0bf615
@Fulanko
added outline of intaRNA prediction to dotplot
8047b4d
@Fulanko
Merge branch 'dev' into basepair-probs
0b6bc63
Fulanko and others added 28 commits February 11, 2020 17:54
@Fulanko
getOverlappingSeed
149d89f
@martin-raden
twaks and todos
24fb307
@Fulanko
PredictionTrackerBPProb fixed ZNL:seed:ZNR case + added seedHandler.i…
f848f24 
…sSeedBasePair()
@Fulanko
basepairProb tracker bug fixes
471f6ad
@Fulanko
predictionTrackerBPprob
9946f4b
@martin-raden
fixes...
275ab07
@martin-raden
input check
f111b62
@martin-raden
fix the fix
666eded
@Fulanko
cleanup
97d6e16
@martin-raden
bugfix
9996634
@Fulanko
fixed bug in ZHR computation
bedb477
@Fulanko
new variant (has missing cases?)
d1d2a2d
@Fulanko
added missing case
abb5f74
@Fulanko
ZR memoization
e0f640f
@Fulanko
Merge branch 'dev' into basepair-probs
21f7909
@Fulanko
added includeBoundaries bool to isSeedBP
6fcbadc
@Fulanko
updateToNextSeedWithK
c7473ee
@martin-raden
seedhandler extension
08b3309
@Fulanko
added SVG dotplots with accessibility energies
b1da844
@Fulanko
improved SVG output
6959b99
@Fulanko
fixed MFE in svg output + moved back to inline css
8b0e5a2
@martin-raden
bugfix
3970230
@Fulanko
svg output fix + changes
6985b91
@Fulanko
Merge branch 'basepair-probs' of github.com:Fulanko/IntaRNA into base…
de409bf 
…pair-probs
@Fulanko
fixed text positioning
fbc5a7f
@martin-raden
box function return now std::string
9b7b426
@martin-raden
fprintf() formatting corrected
cea4ea1
@martin-raden
basepairprob parameter docu extended
a58f38e
@martin-raden martin-raden changed the base branch from dev-frank to master April 29, 2024 14:23
@martin-raden martin-raden changed the base branch from master to dev-frank April 29, 2024 14:30
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2 participants
@martin-raden @Fulanko