Publications by Bin He
C. auris within species evolution of the HIL family
Goal Analyze the evolution of sequence features of the XP_028889033 homologs within C. auris species. In particular, we are interested in intra-species variation in copy number, NTD protein sequence evolutionary rates, stalk repeat numbers and sequences. Homologs identification Homologs of the PF11765 domain containing proteins were identified i...
55606 sym R (22042 sym/43 pcs) 10 img
CTA1 induction in msn2/4 deletion mutants
library(tidyverse) library(ggplot2) library(dplyr) library(mgcv) library(broom) Import data Bash pre-process the data files The data files are organized in three folders under data/d06..., each corresponding to a replicate experiment of the same design. Within each folder, the separate CSV files are the different time points. In this case becau...
10294 sym R (4404 sym/15 pcs) 3 img
_C. auris_ Hil-like proteins prediction
Prepare data Get proteomes from ftp C. auris proteome files were retrieved from NCBI ftp sites and stored in the data/proteome-fasta folder. The concatenated fasta file is stored in the same folder. Write a fasta file I wrote a combined fasta file using the command fwrite(x = Caurisfasta.table[, c(1,3)], file = “Cauris.txt”, sep = ", col.na...
86634 sym R (28362 sym/66 pcs) 11 img 1 tbl
CTT1 and CTA1 induction under no Pi in S. cerevisiae
suppressPackageStartupMessages(library(tidyverse)) Warning message: In if (charToRaw(x) < 20) paste("\\u", toupper(format(as.hexmode(as.integer(charToRaw(x))), : the condition has length > 1 and only the first element will be used suppressPackageStartupMessages(library(cowplot)) suppressPackageStartupMessages(library(GEOquery)) suppressPackage...
15323 sym R (4963 sym/22 pcs) 5 img 1 tbl
20210930-learn-to-analyze-flow-data-with-flowCore
require(tidyverse) Loading required package: tidyverse Registered S3 methods overwritten by 'dbplyr': method from print.tbl_lazy print.tbl_sql ── Attaching packages ───────────────────────────────────────────────────�...
23103 sym R (7912 sym/47 pcs) 10 img
OSR gene induction under phosphate starvation
Goal Plot the induction of oxidative stress response genes in C. glabrata during phosphate starvation. Genes known to be induced during hydrogen peroxide stress in S. cerevisiae are the basis for selecting the candiate gene set. Data C. glabrata -Pi time course Load normalized gene counts for the -Pi time course in C. glabrata. Data collected i...
22539 sym R (9320 sym/16 pcs) 6 img 2 tbl
2022-04-01 Pho4 chimera flow analysis QC
require(tidyverse) Loading required package: tidyverse Registered S3 methods overwritten by 'dbplyr': method from print.tbl_lazy print.tbl_sql ── Attaching packages ───────────────────────────────────────────────────�...
23125 sym R (9182 sym/33 pcs) 14 img