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alphapeptstats

Python Package for the downstream analysis of mass-spectrometry-based proteomics data

camotss

Detection and couting alternative TSS in single cells

denr

Select the most actively transcribed transcript model using PRO-seq

efficient-rna-polymerase-ii-pause-release-requires-u2-snrnp-function_2021

Caizzi, Monteiro-Martins (2021)

grein

GREIN : GEO RNA-seq Experiments Interactive Navigator

ibaqpy

Absolute quantification package based on MSsstats output and Quantms

igv.js-jupyter

Extension for Jupyter Notebook which integrates igv.js

maxquant_and_paw

Compares PAW and MQ for a 7-channel TMT experiment; compares edgeR to two-sample t-test

molpc-2

Modelling of Large Protein Complexes

msstats

R package - MSstats

msstatsshiny_jan2024_copy

R-Shiny GUI integrated with the MSstats package family

nascentrnasim

A package for empirical simulation of nascent RNA data

perseuspy

Integration between Perseus and Python

perseusr

R package for easy interop between Perseus and R

plugininterop

Enables working with external scripts and tools from within Perseus

proactiv

Estimation of Promoter Activity from RNA-Seq data

proteinorm

proteoda

rg4detector

speedppi

Rapid protein-protein interaction network creation from multiple sequence alignments with Deep Learning

tssr