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pfb2022

Programming for Biology Class @ CSHL 2022

phylogenetics

Workshop materials

phylogenomics

introduction to phylogenetics and phylogenomics

pmg

This repo contains scripts used for the identification of phylogenetic marker genes (PMGs) in assembled metagenomic data. Code is provided for benchmarking this method on sequenced genomes as well as running this analysis on metagenomic data. These scripts are in development.

pnu-winter-workshop-2019

Programming code for analyzing the genomic data in PNU winter workshop 2019

practical-data-analysis

Short course using RStudio for biological data analysis

practicalgg

Practical ggplot2

prob140-textbook

Textbook for Stat 140

probabilistic-programming-and-bayesian-methods-for-hackers

aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)

productivity_tools_tricks

Some tools and tricks that I find useful in my daily work

prokamers

Code for kmers in genomes

proteinevolutiontoolbox

protgauss

Gaussian representation of protein sequences to predict nucleosome-binding modes of transcription factors

pybioinformatics

introduction to Python for biologists

pymc3_datasciencela

PyMC3 tutorial for DataScience LA (January 2017)

pymc3_euss

Course in Probabilistic Programming in Python for the 2018 EU Summer School

pytorch-deep-learning

Deep Learning (with PyTorch)

pytorch-seq2seq

Tutorials on implementing a few sequence-to-sequence (seq2seq) models with PyTorch and TorchText.

r_bioinformatic_scripts

R scripts related to bioinformatic analyses. See https://github.com/BIGslu for most recent versions

rate_variability_variation

Code and data for Jackson et al., Intermediate divergence levels maximize the strength of structure–sequence correlations in enzymes and viral proteins, Protein Science, in press.

rates_measurement

repeats

Find longest substring that is repeated specified number of times in a set of documents

reproducible_research

rna-seq-analysis

RNAseq analysis notes from Ming Tang

rna-seq-example

An analysis of Arabidopsis RNA-seq data (hy5 mutant and wt, two replicates each; SRA accession SRX029582)

rna_2021

RNa analysis workshop 2021

rnaseq

RNA-seq analyses.

rnaseq-r

RNAseq analysis in R workshop

rnaseq-recompute-analysis

Analysis of RNA-seq recompute expression data

rnaseq_workshop