davfre

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

stephenturner

## RNA-seq analysis with DESeq2
## Stephen Turner, @genetics_blog

# RNA-seq data from GSE52202
# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with
# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl")

# Import & pre-process ----------------------------------------------------

# Import data from featureCounts

slowkow

#' Convert counts to transcripts per million (TPM).
#' 
#' Convert a numeric matrix of features (rows) and conditions (columns) with
#' raw feature counts to transcripts per million.
#' 
#'    Lior Pachter. Models for transcript quantification from RNA-Seq.
#'    arXiv:1104.3889v2 
#'    
#'    Wagner, et al. Measurement of mRNA abundance using RNA-seq data:
#'    RPKM measure is inconsistent among samples. Theory Biosci. 24 July 2012.

crazyhottommy

#!/bin/bash
# function Extract for common file formats

function extract {
 if [ -z "$1" ]; then
    # display usage if no parameters given
    echo "Usage: extract <path/file_name>.<zip|rar|bz2|gz|tar|tbz2|tgz|Z|7z|xz|ex|tar.bz2|tar.gz|tar.xz>"
 else
    if [ -f "$1" ] ; then
        NAME=${1%.*}

stephenturner

This list is outdated. This post has a list of bioinformatics/genomics/genetics workshops and training materials that I haven't updated since 2015.

---

In-person courses

Note that many of the courses shown below also have course materials from past years publicly available online.

Cold Spring Harbor Courses:

gireeshkbogu

library(ggplot2)

# plot volcano plot
res <- read.table("Male_vs_Female_Pre", head=TRUE)
res$Significant <- ifelse(res$adj.P.Val < 0.05, "adj.P.Val < 0.05", "Not Significant")
ggplot(res, aes(x = logFC, y = -log10(P.Value))) +
  geom_point(aes(color = Significant)) +
  scale_color_manual(values = c("red", "grey")) +
  theme_bw(base_size = 12) + theme(legend.position = "bottom") +
  geom_text_repel(