mfansler

test.mantel <- function (counts, rowScores = NULL, colScores = NULL) {
  ## This implements an ordinal chi-square test following Mantel, 1963,
  ## as described in Agresti, 2007, section 2.5.1 "Linear Trend Alternative to
  ## Independence"
  
  METHOD <- "Mantel's Ordinal Chi-Square Test"
  DNAME = deparse(substitute(counts))
  
  n = sum(counts) # total obs
  if (n < 30)

mfansler

#!/bin/bash                                                                                                                                    

if [ "$#" -ne 1 ]; then
  echo -e "Incorrect number of parameters! Usage:\n    index-gtf.sh <file.gtf(.gz)>" >&2
  exit 1
fi

gtf="$1"

if [[ $gtf =~ \.gz$ ]]; then

mfansler

gzip -cd gencode.vM19.annotation.gtf.gz | 
  awk '$0 !~ /mRNA_end_NF/' | 
  sort -k1,1 -k4,4n | 
  bgzip -@4 > gencode.vM19.mRNA_end_found.gtf.gz

tabix gencode.vM19.mRNA_end_found.gtf.gz

mfansler

#!/usr/bin/env bash

# Example Usage
# ./extract_10X_cell.sh possorted_genome_bam.bam GCCAAATTCACATACG | samtools view -b > cell.bam
#
# Compare with 10X post:
# https://kb.10xgenomics.com/hc/en-us/articles/360022448251-Is-there-way-to-filter-the-BAM-file-produced-by-10x-pipelines-with-a-list-of-barcodes-

if [ "$#" -ne 2 ]; then
  echo -e "Incorrect number of parameters! Usage:\n    extract_10X_cell.sh <file.bam> <cell_bx>" >&2

mfansler

library(tidyverse)

# values at which to evaluate
# this can be changed arbitrarily
x <- c(1,2,3) 

# evaluate y's for every condition and output a long format table
df <- expand.grid(coef=c(1,2), pow=c(1,2,3)) %>%
  group_by(coef, pow) %>%
  mutate(y=map2(coef, pow, ~ tibble(x=x, y=.x*x^.y))) %>%

mfansler

name: genewalk
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - pandas
  - networkx>=2.1
  - gensim
  - goatools

mfansler

name: kallisto-build
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - autoconf
  - automake
  - hdf5
  - make

mfansler

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (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)

mfansler

#!/usr/bin/env awk -f
#' Author: Mervin Fansler
#' GitHub: @mfansler
#' License: MIT
#' 
#' Basic usage
#' $ conda list --export | awk -f list_export_to_yaml.awk
#' 
#' Omitting builds with 'no_builds'
#' $ conda list --export | awk -v no_builds=1 -f list_export_to_yaml.awk

mfansler

name: so-seurat
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _r-mutex=1.0.1=anacondar_1
  - bwidget=1.9.14=0
  - bzip2=1.0.8=haf1e3a3_3
  - c-ares=1.16.1=haf1e3a3_3