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pancancer

Building classifiers using cancer transcriptomes across 33 different cancer-types

pancanstem_web

pandoc

Universal markup converter

paretoti

R toolbox for Archetypal Analysis and Pareto Task Inference on single cell data (based on ParTI)

patchwork

The Composer of ggplots

pd1_analysis_cellcnn

Code to run CellCnn analyses in collaboration paper by Krieg et al. (2018), Nature Medicine

pdl1io

radiomics predictor for non-small cell lung cancer treated with pd1/pdl1 inhibitor immunotherapy

peace_melanoma_14_paper

pi3kd_2022

This repository contains scripts to perform the data analysis of our PI3Kd paper.

piano

piano - An R/Bioconductor package for gene set analysis

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.

pindel-tool

pipelines-wrappers

ATACseq, ChIPseq, RNAseq, WGS, PLAR and cisVar pipeline wrappers

pipipes

piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School

piranha

Piranha is a peak-caller for CLIP- and RIP-seq data

plotluck

R tool for automated creation of ggplots. Examines one, two, or three variables and creates, based on their characteristics, a scatter, violin, box, bar, density, hex or spine plot, or a heat map. Also automates handling of observation weights, log-scaling of axes, reordering of factor levels, and overlays of smoothing curves and median lines.

pmtnet

Deep Learning the T Cell Receptor Binding Specificity of Neoantigen

pnet_prostate_paper

P-NET, Biologically informed deep neural network for prostate cancer classification and discovery

polymorphicherv

Mining mapped reads for accurately predicting polymorphic human endogenous retroviruses

porpoise

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

prad_signature

Prostate Cancer Alteration Signature Analysis

prep

PREP: Prioritizing of RNA Editing-based Peptides

projectils

Interpretation of T cell states using reference single-cell atlases

psi

PSI calculation script

pubs

Repository for scripts, etc. associated with publications.

pum_study

Code to analyze RNA-seq, BRIC-seq, RIP-seq

pyega

EGA (European Genome-phenome archive) downloader

pyradiomics

Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks. Support: https://discourse.slicer.org/c/community/radiomics

qupath

Quantitative Pathology

r-graph-gallery

A website that displays hundreds of R charts