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#! /usr/bin/perl | |
# This script maps oligonucleotides. (i.e.) restriction site, | |
# which are normally to short to be mapped by conventional | |
# methods. | |
# NOTE, incomplete have to add palindrome | |
# subroutine | |
use strict; use warnings; | |
use Getopt::Long; |
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library(DESeq2) | |
library(arrayQualityMetrics) | |
library(gplots) | |
library(RColorBrewer) | |
library(biomaRt) | |
library(ReportingTools) | |
library(org.Mm.eg.db) | |
library(plyr) | |
library(pathview) | |
setwd("C:/Users/Yaroslav/Dropbox/Jacobs_project/") |
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library(DEXSeq) | |
library(pasilla) | |
setwd("/path/to/dir") | |
# Doing the vignette | |
# Get locations for count files and flattened annotation file in gff formar | |
inDir = "~/Dropbox/Jacobs_project/relative_exon_usage/exon_counts" | |
countFiles = list.files(inDir, pattern="exon.txt$", full.names=TRUE) | |
countFiles |
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# Go through vignette | |
library(DiffBind) | |
library(ChIPpeakAnno) | |
library(org.Mm.eg.db) | |
library(KEGG.db) | |
library(reactome.db) | |
setwd("~/Projects/grey_miseq/diffbind_analysis/") | |
# Analyze real samples | |
setwd("~/Projects/grey_miseq/diffbind_analysis/") |
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library("topGO") | |
library("ChIPpeakAnno") | |
library("org.Mm.eg.db") | |
library("plyr") | |
## Get universe ids | |
x <- org.Mm.egGO | |
mapped_genes <- mappedkeys(x) | |
universeIDs <- unique(mapped_genes) |
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library(GenomicFeatures) | |
library(TxDb.Mmusculus.UCSC.mm10.knownGene) | |
library(BSgenome.Mmusculus.UCSC.mm10) | |
library(Biostrings) | |
# Fetch promoter sequences to detect enriched transcription factor | |
# motifs in the promoters of differentially expressed genes | |
setwd("/path/to/dir") | |
list.files() |
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#! /usr/bin/perl | |
# Grab lines between 2 matches and print them out | |
# In this case I'm using it to print out read length | |
# distribution from FastQC's fastqc_data.txt | |
my $dir = shift; # take directory name | |
open ( my $reads_file, "<", "$dir/fastqc_data.txt" ) or die "Cannot open original reads file: $!\n"; | |
# Extract number of reads |
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library(edgeR) | |
library(reshape2) | |
library(plyr) | |
# Get library distribution profile | |
setwd("~/Projects/Champion_smallRNA/length_distr/") | |
list.files() | |
d <- readDGE(list.files(), columns = c(1,2)) | |
counts <- d$count |
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heatmap.2(as.matrix(res), scale = "row", col = redgreen(75), | |
ColSideColors=color_vector, trace = "none", | |
margins = c(14, 13), cexRow = 0.7) |
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########################################################################### | |
## Exploratory analysis | |
library(edgeR) | |
library(DESeq2) | |
library(arrayQualityMetrics) | |
library(gplots) | |
library(RColorBrewer) | |
library(ggplot2) | |
setwd("~/Projects/Champion_smallRNA/comparisons") |