chasemc’s gists

chasemc / 16S_Local-BLAST.rmd

Last active June 27, 2018 00:29

Messy little script to run local BLAST against 16S database

	---
	title: "16S"
	author: "Chase Clark"
	date: "May 15, 2018"
	output: html_document
	---

	```{r eval=FALSE}
	# download file
	#download.file(url = "ftp://ftp.ncbi.nlm.nih.gov/blast/db/16SMicrobial.tar.gz", destfile = "16SMicrobial.tar.gz", mode = 'wb')

chasemc / fast_pvclust.r

Last active July 5, 2018 23:15

fast pvclust

	# library(wordspace)
	# library(pvclust)

	# largeMatrix is a matrix, where rows are samples and columns are variables

	cosineDistanceFunction <- function(x) wordspace::dist.matrix(x, method = "cosine", as.dist = TRUE)

	results <- pvclust(largeMatrix, method.dist = cosineDistanceFunction, nboot=1000)

chasemc / findmzXMLsha.r

Created September 17, 2018 21:26

This gets the sha1 [single] (SHA of entire mzXML file up the SHA1 node) and the filesha1 [maybe multiple] (the SHA of the original data files)

	# requires xml2 and magrittr

	findmzXMLsha <- function(singlemzXMLpath){

	sha <- list(sha1 = NA, filesha1 = NA)

	singlemzXMLpath %>%
	xml2::read_xml() %>%
	xml2::xml_ns_strip() %>%
	xml2::xml_find_first(., "//mzXML/sha1" ) %>%

chasemc / readmzXML.r

Created September 22, 2018 04:26

read mzxml into R for serialization faster than with xml2::serialize

	# a <- path to mzXml

	a %>%
	readLines %>%
	serialize(., NULL) %>%
	memCompress(., type = "gzip") %>%
	list(.) %>%
	return(.) -> d

chasemc / auto_prior.rmd

Created December 19, 2018 23:37

auto_prior

	---
	title: "Sponge Picking"
	author: "Chase Clark"
	date: "November 4, 2018"
	output: html_document
	---

	```{r setup, include=FALSE}
	knitr::opts_chunk$set(echo = TRUE)
	```

chasemc / MALDI_Processing_ShinyApp.R

Created February 6, 2019 22:46

Shiny-modules display of MALDIquant spectrum processing steps

	library(shiny)
	library(MALDIquant)
	library(shinyBS)

	#' QC module variance and smoothing
	#'
	#' @param id namespace
	#'
	#' @return modulke UI
	#' @export

chasemc / bin.R

Created March 12, 2019 22:23

Mass Binning



	#' binnR
	#'
	#' @param vectorList NA
	#' @param ppm NA
	#' @param massStart NA
	#' @param massEnd NA
	#'
	#' @return NA

chasemc / boxplotRant.Rmd

Created March 30, 2019 01:27

boxplotRant.Rmd

	---
	title: "Untitled"
	author: "Chase Clark"
	date: "March 29, 2019"
	output: html_document
	---


	```{r}
	library(ggpubr)

chasemc / sparseMatrix.csv

Created April 2, 2019 21:05

We can't make this file beautiful and searchable because it's too large.

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chasemc / sparseMatrix.csv

Created April 2, 2019 21:05

We can't make this file beautiful and searchable because it's too large.

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Chase Clark chasemc