Publications by Bin He
E041 SYTO9+PI vs PI alone, 2024-01-24
Background This is the flow cytometry data for miglog phase Cg stained with PI/PI+SYTO9/ SYTO+PI in different staining orders, and run through flow cytometry (details in ELN). The goal is to establish FungaLight’s distinguishing power with different staining protocols. require(tidyverse) require(flowCore) require(flowClust) require(openCyto) requ...
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20201223-Pho4-GFP-plasmid-leu2-test-reanalyze
require(tidyverse) Loading required package: tidyverse ── Attaching core tidyverse packages ────────────────────────────────────────────────────────────────────────────────────�...
27234 sym Python (8573 sym/12 pcs) 11 img 1 tbl
20201221-Pho4-GFP-plasmid-leu2-test-reanalyze
require(tidyverse) require(cowplot) Goal After determining that I can take the cells directly from the media to the flow cytometer, by diluting them in the original media or just PBS, I decided to repeat the previous experiment, this time dropping the endogenous set (in retrospect should have kept them in) and added newly obtained plasmid-Pho4-GFP...
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20230302-E036-ASR-plot-stat-test
require(tidyverse) require(cowplot) Introduction Goal Plotting ASR data for Fig. 1, S1, … Data Jinye’s table goes here Read in data tmp <- read_tsv("../input/20220726-ASR-CFU-raw.tsv", col_types = cols(), comment = "#") raw <- read_csv("../input/20221224-ASR-CFU-raw.csv", col_types = cols(), comment = "#") %>% mutate(Date = gsub("d(\\d\\d...
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Learning how to cluster gene expression data
library(tidyverse) Registered S3 methods overwritten by 'dbplyr': method from print.tbl_lazy print.tbl_sql ── Attaching packages ─────────────────────────────── tidyverse 1.3.0 ── ✓ ggplot2 3.3.2 ✓ purrr 0.3.4 ✓ tibble 3.0.1 ✓ dplyr ...
32064 sym R (10114 sym/48 pcs) 17 img
BLAST search to identify homologs for XP_028889033
This analysis accompanies the BLAST search to identify homologs for XP_028889033 suppressPackageStartupMessages(library(tidyverse)) # install rentrez package if not already installed if (!requireNamespace("rentrez", quietly = TRUE)) install.packages("rentrez") suppressPackageStartupMessages(library(rentrez)) # set NCBI Entrez API key set_entr...
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20201223 repeat flow cytometry for Pho4-GFP
require(tidyverse) require(cowplot) Goal This is to repeat the 2020-12-21 experiment. Material and methods See gDoc. This time I reverted to one o/n growth. The second growth was done in the 96-well clear plate (not deep well). Cells were directly diluted into PBS and run on the flow cytometer. Table of strains Data and analysis Import data ...
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20201215 Pho4-GFP integration with PHO5pr-mCherry test
require(tidyverse) require(cowplot) Goal Testing the brightness of Pho4-GFP (mNeon and EGFP) either on a plasmid or integrated at the leu2 or endogenous Pho4 locus. also evaluate the population heterogeneity and use the PHO5pr-mCherry reporter to evaluate the functionality of the Pho4 variants Material and methods table of strains methods See...
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20201221-Pho4-GFP-plasmid-leu2-test
require(tidyverse) require(cowplot) Goal After determining that I can take the cells directly from the media to the flow cytometer, by diluting them in the original media or just PBS, I decided to repeat the previous experiment, this time dropping the endogenous set (in retrospect should have kept them in) and added newly obtained plasmid-Pho4-G...
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2021-03-19 reanalyze Jia and Lindsey's flow cytometry data from 20210310
require(tidyverse) Loading required package: tidyverse Registered S3 methods overwritten by 'dbplyr': method from print.tbl_lazy print.tbl_sql ── Attaching packages ───────────────────────────────────────────────────�...
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