The goal of yeastgenes is to provide gene expression data from yeast.
Installation
You can install the development version of yeastgenes from GitHub with:
# install.packages("pak")
pak::pak("rnabioco/yeastgenes")Example
library(yeastgenes)
yeast_gene_exp
#> # A tibble: 199,296 × 4
#> systematic_name nutrient rate exp
#> <chr> <fct> <fct> <dbl>
#> 1 YPR204W Glucose 0.05 1.17
#> 2 YPR204W Glucose 0.1 1
#> 3 YPR204W Glucose 0.15 0.86
#> 4 YPR204W Glucose 0.2 0.77
#> 5 YPR204W Glucose 0.25 0.53
#> 6 YPR204W Glucose 0.3 0.3
#> 7 YPR204W Ammonia 0.05 2.79
#> 8 YPR204W Ammonia 0.1 2
#> 9 YPR204W Ammonia 0.15 0.6
#> 10 YPR204W Ammonia 0.2 0.16
#> # ℹ 199,286 more rows
yeast_go_terms
#> # A tibble: 5,537 × 4
#> systematic_name common_name go_molecular_function go_biological_process
#> <chr> <chr> <chr> <chr>
#> 1 YNL049C SFB2 molecular function unknown ER to Golgi transport
#> 2 YNL095C <NA> molecular function unknown biological process u…
#> 3 YDL104C QRI7 metalloendopeptidase activ… proteolysis and pept…
#> 4 YLR115W CFT2 RNA binding mRNA polyadenylylati…
#> 5 YMR183C SSO2 t-SNARE activity vesicle fusion*
#> 6 YML017W PSP2 molecular function unknown biological process u…
#> 7 YOL066C RIB2 pseudouridylate synthase a… riboflavin biosynthe…
#> 8 YPR036W VMA13 hydrogen-transporting ATPa… vacuolar acidificati…
#> 9 YEL015W EDC3 molecular function unknown deadenylylation-inde…
#> 10 YOR069W VPS5 protein transporter activi… protein retention in…
#> # ℹ 5,527 more rows
yeast_prot_props
#> # A tibble: 6,724 × 38
#> systematic_name mw pi protein_length n_term_seq c_term_seq gravy_score
#> <chr> <dbl> <dbl> <dbl> <chr> <chr> <dbl>
#> 1 YFL011W 60676. 9.11 546 MVSSSVS LVIVDSK 0.42
#> 2 YFL012W 17186. 9.76 148 MPKSRPK LRSFQNF -0.78
#> 3 YER006W 57716. 9.44 520 MRVRKRQ DQDTMME -0.58
#> 4 YDR001C 85881. 7.88 751 MSQVNTS ERNLYGL -0.54
#> 5 YER007C-A 20277. 7.06 181 MFKKFTR LWNFSVE -0.18
#> 6 YDR002W 22950. 5.89 201 MSSEDKK QEINKKA -0.99
#> 7 YER009W 14446. 4.29 125 MSLDFNT FRLNYSA -0.39
#> 8 YDR005C 44724. 4.89 395 MKFIDEL DQEESLQ -0.86
#> 9 YLR440C 82353. 4.53 709 MLEEQLY FHNVTNF -0.27
#> 10 YLR441C 28764. 10.8 255 MAVGKNK DEVLETV -0.49
#> # ℹ 6,714 more rows
#> # ℹ 31 more variables: aromaticity_score <dbl>, cai <dbl>, codon_bias <dbl>,
#> # fop_score <dbl>, ala <dbl>, cys <dbl>, asp <dbl>, glu <dbl>, phe <dbl>,
#> # gly <dbl>, his <dbl>, ile <dbl>, lys <dbl>, leu <dbl>, met <dbl>,
#> # asn <dbl>, pro <dbl>, gln <dbl>, arg <dbl>, ser <dbl>, thr <dbl>,
#> # val <dbl>, trp <dbl>, tyr <dbl>, carbon <dbl>, hydrogen <dbl>,
#> # nitrogen <dbl>, oxygen <dbl>, sulphur <dbl>, instability_index_ii <dbl>, …