In GreshamLab/labtools: Useful Tools for the Gresham Lab

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(labtools)

This vignette provides examples of how to use functions in the package labtool, which includes a set of useful functions developed in the Gresham Lab.

Available functions inlclude:

1. gff_from_snapgene_features()
2. hello()
3. std_err()
4. yeast_common_to_sgd()
5. yeast_common_to_systematic()
6. yeast_gene_names()
7. yeast_r64_to_systematic()
8. yeast_sgd_to_common()
9. yeast_sgd_to_systematic()
10. yeast_systematic_to_common()
11. yeast_systematic_to_sgd()

to install this package and vignette:

library(devtools) install_github("GreshamLab/labtools", build_vignettes = TRUE)

to view vignette:

help(package = 'labtools', help_type = 'html')

or

vignette("labtool-vignette")

Below are some examples of how to use the functions and the expected output

1. How to make a gff from a snap gene file.

To run this example, download an example file (SnapBarcodeLibrary1.csv) from here

make_gff_from_snap(file_path = "../../data/SnapBarcodeLibrary1.csv", chromosome = "II", feature_source = "levy_bc", output = "../../data/Barcode.gff")

The resulting gff (Barcode.gff) should be a plain text tab delimited file that looks like like this:

file.show('../../data/Barcode.gff')

II  levy_bc misc_feature    1001    1003    .   +   .   YBR209W
II  levy_bc misc_feature    1004    1028    .   +   .   PEV9
II  levy_bc misc_feature    1036    1514    .   +   .   GAL1 promoter
II  levy_bc misc_feature    1611    2642    .   +   .   Cre
II  levy_bc misc_feature    2133    2153    .   +   .   P23
II  levy_bc misc_feature    2960    3211    .   +   .   CYC1 terminator
II  levy_bc misc_feature    3220    3253    .   +   .   lox66/71
II  levy_bc misc_feature    3233    3240    .   +   .   LoxP core
II  levy_bc misc_feature    3262    3513    .   -   .   CYC1 terminator
II  levy_bc misc_feature    3831    4057    .   -   .   Cre (truncated)
II  levy_bc misc_feature    4088    4566    .   -   .   GAL1 promoter
II  levy_bc misc_feature    7765    8715    .   -   .   HygMX
II  levy_bc misc_feature    9174    9308    .   +   .   URA3 promoter
II  levy_bc gene    9309    9497    .   +   .   URA3
II  levy_bc misc_feature    9498    9503    .   +   .   Artificial Intron Start
II  levy_bc misc_feature    9503    9527    .   +   .   Forward Sequencing Primer
II  levy_bc misc_feature    9552    9577    .   +   .   BC2
II  levy_bc misc_feature    9578    9611    .   +   .   loxP
II  levy_bc misc_feature    9591    9598    .   +   .   loxP core
II  levy_bc misc_feature    9612    9637    .   +   .   BC1
II  levy_bc misc_feature    9646    9669    .   +   .   Reverse Sequencing Primer
II  levy_bc misc_feature    9675    9681    .   +   .   Artificial intron branch point
II  levy_bc misc_feature    9700    9702    .   +   .   Artificial intron terminator
II  levy_bc misc_feature    9703    10317   .   +   .   URA3
II  levy_bc misc_feature    10318   10394   .   +   .   URA3 terminator
II  levy_bc gene    10754   11563   .   +   .   kanMX
II  levy_bc misc_feature    11696   11715   .   +   .   NatMx
II  levy_bc misc_feature    11696   11715   .   -   .   PEV8
II  levy_bc misc_feature    11716   11718   .   +   .   YBR209W`

GreshamLab/labtools documentation built on Feb. 18, 2022, 12:16 p.m.