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phageparser

A project to extract CRISPR information from open genetic data.

phonemes

code for PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry), a method to model signalling networks based on untargeted phosphoproteomics

php-markdown

Parser for Markdown and Markdown Extra derived from the original Markdown.pl by John Gruber.

php-src

The PHP Interpreter

phyloseqgraphtest

phyltr

Unix filters for manipulating and analysing (samples of) phylogenetic trees represented in the Newick format

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

picobio

Miscellaneous Bioinformatics scripts etc mostly in Python

picrust

Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tests

pig

Mirror of Apache Pig

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

pipelines-api-examples

Examples for the Google Genomics Pipelines API.

pipelines_for_chip-seq_analysis

Pipelines for ChIP-seq analysis, such as peak calling, differential enrichment detection, and pausing index calculation for PolII.

planemo

Command-line utilities to assist in developing tools for the Galaxy Project.

plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase).

ploscompsomiteclocknoise

Sample of data from the PLoS Computational Biology Paper, 'Stochastic Regulation of her1/7 Gene Expression is the Source of Noise in the Zebrafish Somite Clock Counteracted by Notch Signalling'.

plottree

plyr

A R package for splitting, applying and combining large problems into simpler problems

pmsignature

R package for extracting mutation signatures from a list of somatic mutations

pmsignature_shiny

shiny programis for pmsignature

pmtk3

Probabilistic Modeling Toolkit for Matlab/Octave.

pointwise-influence-matrices

Data and code for "Pointwise influence matrices for functional-response regression". Preprint available at https://works.bepress.com/phil_reiss/43/

polar-code

polarcodes

Polar code implementation in C

polyfreqs

polyfreqs: an R package for Bayesian population genomics in autopolyploids

polyphen2

applying polyphen_2 score to predict functional impact for a given gene

pose

Phenotype-Optimized Sequence Ensembles

predictgestationalage

Predict Gestational Age from Cord Blood Methylation

predictive-model-for-cancer-detection-using-mirna

This is a predictive model built using various machine learning algorithms to predict the type of cancer using miRNA in blood plasma or serum using the technology of "liquid biopsy".

predixcan

PrediXcan Project