slavailn’s gists

slavailn / edgeR_GLM_smallRNA.R

Created February 20, 2019 23:39

Edger GLM approach with 2 treatments over 3 time-points on small RNA tags

	library(edgeR)

	setwd(<dir>)

	files <- list.files("/tag_counts/", full.names = T) # tab delimited file with sequenca tags and raw counts
	files
	d <- readDGE(files, columns = c(1,2))
	counts <- d$counts
	sampleFile <- <sampleFile>
	sampleInfo <- read.table(sampleFile, sep = "\t", header = T, stringsAsFactors = F)

slavailn / get_bwa_mapping_stats.sh

Created January 17, 2019 21:49

Get BWA mapping stats (mapped, unmapped reads, number of reads with MAPQ20)

	#! /bin/bash

	echo -e "Samplename\tTotal_reads\tMapped_reads\tUnmapped_reads\tMAPQ20_reads\tPercent_mapped\tPercent_MAPQ20_reads"

	for file in ./*bam
	do
	filename=`basename $file`
	samplename=${filename%.bam}
	total_reads=`samtools view -c $file`
	mapped_reads=`samtools view -c -F 4 $file`

slavailn / Process_ChIP-seq_peaks.R

Created January 14, 2019 22:20

Process ChIP-seq peaks, based on multiple Bioconductor packages, but centered on ChipSeeker and ClusterProfiler

slavailn / ChipSeeker_vignette.R

Created January 10, 2019 23:00

Going through ChIPseeker vignette, will modify as necessary for the actual analysis

	library(ChIPseeker)
	library(TxDb.Hsapiens.UCSC.hg19.knownGene)
	library(clusterProfiler)

	# Gene data from UCSC hg19
	txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

	# Peak file in bed format (these are MACS files)
	files <- getSampleFiles()
	files

slavailn / GenomicDataCommons_rnaseq.R

Created December 21, 2018 22:13

GenomicDataCommons vignette examples and how to download RNA-seq data from GDC

	library(GenomicDataCommons)
	library(DESeq2)
	library(ggplot2)

	setwd("~/Projects/MYT1L_TCGA_project/")

	###############################################################################################
	# Vignette examples
	# Check connectivity and functionality
	GenomicDataCommons::status()

slavailn / plotDMR_ggbio.R

Created December 12, 2018 01:09

plot DMR using ggbio (ggplot type graphics, separate pane for every sample with a bar graph for methylation percent)

	library(GenomicRanges)
	library(ggbio)
	library(ChIPpeakAnno)

	gr <- GRanges(seqnames = "NC_035082.1", IRanges(55355800, 55355870), strand = "*")

	# Get methylation percents from metilene input and convert to GRanges object
	input <- read.table("metilene_Control_Treated.input", sep = "\t", header = T, stringsAsFactors = F)
	names(input)[1] <- "chr"
	names(input)[2] <- "start"

slavailn / ggbio_examples.R

Created December 11, 2018 23:28

Going through code examples in ggbio

slavailn / show_genomic_tracks.R

Created December 10, 2018 22:29

Display genomic tracks - ggbio, sushi

	library(Rsamtools)
	library(rtracklayer)
	library(Sushi)

	# Draw raw alignment track for each bam file
	setwd("~/Projects/Wiseman_Trout_RRBS/")
	list.files("bam")

	# Create TxDb object from GFF
	chromInfo <- read.table("~/GENOMES/Rainbow_trout/GCF_002163495.1_Omyk_1.0_genomic.fa.fai", header = F,

slavailn / forge_BSgenome.R

Created December 7, 2018 00:41

forge BSgenome package for non model organism (Rainbow trout as an example)

	library(BSgenome)

	## Create seed file with the following lines
	# Package: BSgenome.Omykiss.NCBI.Omyk1
	# Title: Full genome sequences for Oncorhynchus mykiss (NCBI RefSeq version Omyk_1.0)
	# Description: Full genome sequences for Oncorhynchus mykiss (Rainbow trout) as provided by MCBI (Omyk_1.0, 2017-6-2) and stored in Biostrings objects.
	# Version: 1.0
	# organism: Oncorhynchus mykiss
	# common_name: Rainbow trout
	# provider: NCBI

slavailn / txdb_non_model.R

Created December 6, 2018 20:45

Create TxDb for non-model organism (example: Rainbow Trout)

	library(GenomicFeatures)


	# Get chromInfo file
	chromInfo <- read.table("~/GENOMES/Rainbow_trout/GCF_002163495.1_Omyk_1.0_genomic.fa.fai", header = F,
	stringsAsFactors = F, sep = "\t")
	head(chromInfo)
	chromInfo <- chromInfo[,c(1,2)]
	names(chromInfo) <- c("chrom", "length")
	is_circular <- rep(FALSE, dim(chromInfo)[1])

slava ilnytskyy slavailn