An R package for biological sequence representations
!!!NOTE: We have tested these codes on Ubuntu 18.04.2 LTS. There is no
guarantee that these codes can be compiled and executed on other
platforms without modifications.(Currently cannot be installed in the
Win) Now, UltraPseR support all platforms.
The development version from github:
if (!requireNamespace("devtools", quietly=TRUE))
install.packages("devtools")
devtools::install_github("YuLab-SMU/UltraPseR")library(dplyr)tiny_sequences <- system.file("extdata", "tiny.fas", package = "UltraPseR")
x <- UltraPseR::UpseR(input = tiny_sequences, module = "comp", note = "stdprot") ## Registered S3 methods overwritten by 'ggalt':
## method from
## grid.draw.absoluteGrob ggplot2
## grobHeight.absoluteGrob ggplot2
## grobWidth.absoluteGrob ggplot2
## grobX.absoluteGrob ggplot2
## grobY.absoluteGrob ggplot2
x## 043L_IIV6|0 094L_IIV6|0
## 1 0.000 1.695
## 2 4.310 3.390
## 3 7.759 3.390
## 4 7.759 5.085
## 5 5.172 3.390
## 6 3.448 3.390
## 7 0.000 2.542
## 8 14.655 11.864
## 9 12.931 11.017
## 10 10.345 9.322
## 11 2.586 4.237
## 12 13.793 14.407
## 13 1.724 0.847
## 14 1.724 2.542
## 15 0.862 1.695
## 16 2.586 7.627
## 17 2.586 5.932
## 18 3.448 2.542
## 19 0.862 0.000
## 20 3.448 5.085
tiny_sequences <- system.file("extdata", "tiny.fas", package = "UltraPseR")
pro <- UltraPseR::UpseR(input = tiny_sequences, note = "stdprot", module = "pse", property = "ZIMJ680105", w = 0.05, l = 10, t = 2)
p <- UltraPseR::plot_upse(pro)
p
DNA_sequences <- system.file("extdata", "tiny-dna.fas", package = "UltraPseR")
dna_res <-UltraPseR::UpseR(input = DNA_sequences, note = "didna", module = "pse", property = "DD0033", w = 0.05, l = 3, t = 1)
p1 <- UltraPseR::plot_upse(dna_res)
p1
UltraPseR::available_prop(note = "didna")## DD0001 Base stacking
## DD0002 Protein induced deformability
## DD0003 B-DNA twist
## DD0004 Dinucleotide GC Content
## DD0005 A-philicity
## DD0006 Propeller twist
## DD0007 Duplex stability (freeenergy)
## DD0008 Duplex stability (disruptenergy)
## DD0009 DNA denaturation
## DD0010 Bending stiffness
## DD0011 Protein DNA twist
## DD0012 Stabilising energy of Z-DNA
## DD0013 Aida_BA_transition
## DD0014 Breslauer_dG
## DD0015 Breslauer_dH
## DD0016 Breslauer_dS
## DD0017 Electron_interaction
## DD0018 Hartman_trans_free_energy
## DD0019 Helix-Coil_transition
## DD0020 Ivanov_BA_transition
## DD0021 Lisser_BZ_transition
## DD0022 Polar_interaction
## DD0023 SantaLucia_dG
## DD0024 SantaLucia_dH
## DD0025 SantaLucia_dS
## DD0026 Sarai_flexibility
## DD0027 Stability
## DD0028 Stacking_energy
## DD0029 Sugimoto_dG
## DD0030 Sugimoto_dH
## DD0031 Sugimoto_dS
## DD0032 Watson-Crick_interaction
## DD0033 Twist
## DD0034 Tilt
## DD0035 Roll
## DD0036 Shift
## DD0037 Slide
## DD0038 Rise
## DD0039 Stacking energy
## DD0040 Bend
## DD0041 Tip
## DD0042 Inclination
## DD0043 Major Groove Width
## DD0044 Major Groove Depth
## DD0045 Major Groove Size
## DD0046 Major Groove Distance
## DD0047 Minor Groove Width
## DD0048 Minor Groove Depth
## DD0049 Minor Groove Size
## DD0050 Minor Groove Distance
## DD0051 PersistanceLength
## DD0052 MeltingTemperature
## DD0053 Mobilitytobendtowardsmajorgroove
## DD0054 Mobilitytobendtowardsminorgroove
## DD0055 PropellerTwist
## DD0056 ClashStrength
## DD0057 Enthalpy
## DD0058 Shift(RNA)
## DD0059 Hydrophilicity(RNA)
## DD0060 Freeenergy
## DD0061 Twist_twist
## DD0062 Tilt_tilt
## DD0063 Roll_roll
## DD0064 Twist_tilt
## DD0065 Twist_roll
## DD0066 Tilt_roll
## DD0067 Shift_shift
## DD0068 Slide_slide
## DD0069 Rise_rise
## DD0070 Shift_slide
## DD0071 Shift_rise
## DD0072 Slide_rise
## DD0073 Twist_shift
## DD0074 Twist_slide
## DD0075 Twist_rise
## DD0076 Tilt_shift
## DD0077 Tilt_slide
## DD0078 Tilt_rise
## DD0079 Roll_shift
## DD0080 Roll_slide
## DD0081 Roll_rise
## DD0082 Slidestiffness
## DD0083 Shiftstiffness
## DD0084 Rollstiffness
## DD0085 Risestiffness
## DD0086 Tiltstiffness
## DD0087 Twiststiffness
## DD0088 Wedge
## DD0089 Direction
## DD0090 Flexibility_slide
## DD0091 Flexibility_shift
## DD0092 Entropy
## Total number of properties : 92