Projects in Awesome Lists by pwilmart

https://github.com/pwilmart/paw_pipeline

A Comet-based, best practices proteomics pipeline.

comet protein-identification protein-inference proteomics python3 tmt

Last synced: 28 Oct 2024

https://github.com/pwilmart/PAW_pipeline

A Comet-based, best practices proteomics pipeline.

comet protein-identification protein-inference proteomics python3 tmt

Last synced: 02 Aug 2024

https://github.com/pwilmart/tmt_analysis_examples

Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.

ipynb jupyter-notebook mass-spectrometry proteomics proteomics-data r tmt tmt-data-analyses

Last synced: 11 Oct 2024

https://github.com/pwilmart/irs_normalization

An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.

ipynb irs-normalization jupyter-notebook mass-spectrometry normalization proteomics proteomics-data r tmt

Last synced: 11 Oct 2024

https://github.com/pwilmart/start_here

Navigation links (and brief descriptions) to my repositories.

Last synced: 11 Oct 2024

https://github.com/pwilmart/Start_Here

Navigation links (and brief descriptions) to my repositories.

Last synced: 02 Aug 2024

https://github.com/pwilmart/fasta_utilities

Utilities for downloading and managing protein FASTA files.

ensembl fasta ncbi protein-databases python3 uniprot

Last synced: 11 Oct 2024

https://github.com/pwilmart/paw_blast

A utility for blasting one protein FASTA file against another FASTA file to find orthologs.

annotations blast proteomics python3

Last synced: 11 Oct 2024

https://github.com/pwilmart/annotations

GUI tool to add rich annotations to PAW summary files from Swiss-Prot flat text files.

orthologs protein-annotations proteomics python3 tkinter-gui

Last synced: 11 Oct 2024

https://github.com/pwilmart/irs_validation

Analysis of technical replicate channels to more fully validate the internal reference scaling (IRS) method.

ipynb irs irs-normalization jupyter-notebook normalization proteomics r tmt tmt-data-analyses

Last synced: 11 Oct 2024

https://github.com/pwilmart/score_distributions_fdr

How relative sizes of incorrect and correct score distributions affect FDR thresholds.

Last synced: 11 Oct 2024

https://github.com/pwilmart/talk_to_repo_example

Example of turning a Powerpoint talk into a repo README.md

github markdown meeting-presentation powerpoint slide-images

Last synced: 11 Oct 2024

https://github.com/pwilmart/recomb-cp_2012

PowerPoint from 2012 RECOMB-CP meeting: shotgun analysis tutorial - mods, accurate mass, FDR

Last synced: 11 Oct 2024

https://github.com/pwilmart/human-plasma_dia-vs-tmt

An apples-to-aardvarks comparison of human plasma proteomes from DIA and TMT

Last synced: 11 Oct 2024

https://github.com/pwilmart/cascadia_2013

2013 Cascadia Proteomics Symposium talk about extended parsimony protein grouping.

Last synced: 11 Oct 2024

https://github.com/pwilmart/utilities

Some Python utility scripts for proteomics file management

file-management proteomics python3 utilities

Last synced: 11 Oct 2024

https://github.com/pwilmart/tmt_paw_pipeline

Details about how TMT labeling is handled in PAW pipeline

Last synced: 11 Oct 2024

https://github.com/pwilmart/cloud_desktop_benchmarks

Benchmarking proteomics analyses on desktop computers and in the cloud.

Last synced: 11 Oct 2024

https://github.com/pwilmart/z-score_gui

GUI app for doing sliding window Z-score transformations of quantitative proteomics data

clipboard gui-application python3 scipy statistical-testing

Last synced: 11 Oct 2024

https://github.com/pwilmart/abrf_iprg_2015_spc

A spectral counting analysis of the ABRF iPRG 2015 study

abrf-study jupyter-notebook paw-pipeline proteomics r specrtal-counting spectral-counts

Last synced: 11 Oct 2024

https://github.com/pwilmart/plubell_2017_paw

Data from Plubell et al., 2017 processed with the PAW pipeline.

irs-normalization jupyter-notebook paw-pipeline proteomics r tmt tmt-data-analysis

Last synced: 11 Oct 2024

https://github.com/pwilmart/cascadia_2018

Using Jupyter notebooks in proteomics data analyses talk slides from the 2018 Cascadia Proteomics Symposium

Last synced: 11 Oct 2024

https://github.com/pwilmart/bcp-all_qe-tmt_nat-comm-2019

Re-analysis of data from childhood acute lymphoblastic leukemia study in Nat. Comm. April 2019

irs-normalization jupyter-notebook paw-pipeline proteomics r tmt tmt-data-analyses

Last synced: 11 Oct 2024

https://github.com/pwilmart/tmt_channel_cross_talk

An exploration of how much TMT channels cross-talk with each other

Last synced: 11 Oct 2024

https://github.com/pwilmart/sea_lion_urine_spc

Sea lion urine comparison with spectral counting.

edger jupyter-notebook paw-pipeline proteomics r spectral-counting spectral-counts

Last synced: 11 Oct 2024

https://github.com/pwilmart/multiple_tmt_mq

Developing mouse lens done with MQ

irs-normalization jupyter-notebook maxquant proteomics r tmt tmt-data-analysis

Last synced: 11 Oct 2024

https://github.com/pwilmart/yeast_carbonsources

Yeast TMT data - 3 different carbon sources (from Gygi lab) analyzed with PAW pipeline and MaxQuant

jupyter-notebook paw-pipeline proteomics r statistical-testing tmt tmt-data-analyses

Last synced: 11 Oct 2024

https://github.com/pwilmart/sps-ms3_vs_ms2_tmt

Comparison of SPS MS3 TMT data to MS2 TMT data

jupyter-notebook proteomics r tmt tmt-data-analysis

Last synced: 11 Oct 2024

https://github.com/pwilmart/maxquant_and_paw

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

comet jupyter-notebook maxquant paw-pipeline proteomics r tmt tmt-data-analysis

Last synced: 11 Oct 2024

https://github.com/pwilmart/pxd017823_real-time-search

Re-analysis of data from PXD017823 exploring real time search for TMT.

Last synced: 11 Oct 2024

https://github.com/pwilmart/human_rhesus_tmt

Analysis discussion of a multi-sample, multi-fraction, multi-kit, multi-species TMTpro experiment

Last synced: 11 Oct 2024

https://github.com/pwilmart/asms_2018

IRS normalization poster presented at 2018 San Diego ASMS meeting (Thursday #389) .

Last synced: 11 Oct 2024

https://github.com/pwilmart/yeast_triple_ko_tmt

R analysis of TMT data from Yeast triple knockout strains (Paulo et al., 2016, JASMS, v27, p1620-25)

irs-normalization jupyter-notebook paw-pipeline proteomics r tmt tmt-data-analysis

Last synced: 11 Oct 2024

https://github.com/pwilmart/dilution_series

Tandem Mass Tag (TMT) dilution series analysis

jupyter-notebook paw-pipeline proteomics r tmt tmt-data-analyses

Last synced: 11 Oct 2024

https://github.com/pwilmart/precursor_mass_corrections

Explores precursor mass correction algorithm assumptions and claims

Last synced: 11 Oct 2024