Kamil Slowikowski
About Archive

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Bash

Print bigWig data for each region in a BED file

Run Picard tools and collate multiple metrics files

featureCounts requires identical mate ids

Make ribosomal RNA intervals for Picard CollectRnaSeqMetrics


Data

Get transcription factor target genes

SNP Proxies

1000 Genomes Allele Frequencies and Linkage Disequilibrium


Javascript

Autocomplete gene names with mygene.info and typeahead.js

SNP Proxies

GTEx RNA-Seq Visualizations


Projects

Determine if a transcription factor is bound with CENTIPEDE

Run Picard tools and collate multiple metrics files


Python

Build bioinformatics pipelines with Snakemake

Join multiple PLINK dosage files into one file

Benchmark the binomial probability mass function in Python

Count the number of coding base pairs in each Gencode gene

0-based and 1-based genomic intervals, overlap and distance


R

Make heatmaps in R

Color points by density with ggplot2

Compare distributions with box plots, not bar plots

Determine if a transcription factor is bound with CENTIPEDE

Get transcription factor target genes

Quickly aggregate your data with data.table in R

Create a quantile-quantile plot with ggplot2


Tutorials

Make heatmaps in R

Color points by density with ggplot2

Build bioinformatics pipelines with Snakemake

Determine if a transcription factor is bound with CENTIPEDE

How to ssh to a remote server without typing your password