• Stars
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    3
  • Rank 3,963,521 (Top 79 %)
  • Language
    Python
  • Created over 5 years ago
  • Updated 9 months ago

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Repository Details

Cancer Analysis tools in Python

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deTiN

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MutSig2CV

MutSig2CV from Lawrence et al. 2014
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dalmatian

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CPTAC_PanCan_PTM_2023

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Haradhvala_et_al_2022

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10x-cd45-isoform-quantification

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CLUMPS-PTM

CLUMPS adapted to post-translational modifications.
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11

ABSOLUTE

ABSOLUTE source code that works with allelic copy ratio on both hg19 and hg38
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12

canine

A modular, high-performance computing solution to run jobs using SLURM
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13

AnnoMate

Review anything (purities, mutations, etc) within a jupyter notebook with plotly dash and jupyter widgets
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14

Boiarsky-etal-2022

Code to reproduce methods & results from Boiarsky et. al., Nature Communications 2022
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15

igv_remote

A Python interface for interacting with IGV desktop over a port using IGV batch commands
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16

SMM_clustering_2020

Repo for analysis of SMM DNA + RNA data.
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17

LUAD_subtypes

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18

CLUMPS

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19

rnaseqc2-paper

RNA-SeQC 2 manuscript materials
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20

pathway_based_biomarker

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21

CLUMPS2

Re-factored code for CLUMPS.
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22

mudi

A collection of downstream python single-cell utilities.
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23

mutect-benchmark

Code repo for master thesis
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24

MSMuTect2

Accurate detection of somatic MS (microsatellite) indels.
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25

CLLmap

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26

PurityReviewer

Suite of purity reviewers and review components
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27

igv_gdc_buddy

stream & update gdc signed url to IGV
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28

gbm_icb_manuscript

Code for reproducing the figures in the Ghannam et al. GBM ICB manuscript
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29

GISTIC2_postprocessing

The repo contains codes (in matlab) to force call GISTIC2 driver events at sample level
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30

lapdog

A python module, CLI, and browser-based UI to run jobs outside of Firecloud
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31

MSMuTect1

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32

MSMuTect

Calling indels in microsatellite loci
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33

REBC_tools

Repo for code & tasks used for REBC analysis
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34

AsymTools2

AsymTools is a package for analyzing transcriptional and replicative mutational strand asymmetries in cancer sequencing datasets.
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35

MSMutSig

Detects loci with a significantly higher-than-expected frequency of somatic MS (microsatellite) indels.
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36

PhylogicNDTReviewer

Interactive app to review Phylogic solutions and data.
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bladder_cancer_classifier

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38

DLBclass-tool

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