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alternative-proteome-detection-project

biosurfer

"Surf" the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.

biosurfer_analysis

This repository reproduces the analysis for biosurfer tool

biosurfer_bmd_analysis

This code repository uses the Biosurfer tool (old version) to conduct NMD and protein truncation analysis for long-read bone proteogenomics project.

coon_isoform_analysis

Looking at things related to data from https://www.nature.com/articles/s41587-023-01714-x#Sec24

huvec-proteogenomic-analysis

HUVEC analysis analyzing proteogenomic data generated from long-read transcriptomic sequencing and bottom-up mass spec data

isoseq-nextflow

Nextflow implementation of IsoSeq3

lime

long-read-proteogenomics

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

long-read-proteogenomics-analysis

pdb-isoform-analysis

Comparison of all available PDB chains (human) to the alternative isoforms in GENCODE.

revio-mas-bulk-benchmark

sheynkman-lab-docs

smc_proteogenomics

splice-event-to-isoform-pipeline

Shay's splice event to isoform integration pipeline

sqanti3-docker

A docker image to run SQANTI3

sqanti3_protein

Repository of SQANTI3 tool for Quality Control of Long-Read Defined Transcriptomes

sqtl_pipeline_v2

Pipeline to map sQTLs to protein isoforms

tappas

This repository contains the source code for the tappAS application. See README for details.