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addwikiusers

Quick and dirty perl script to add new users to a wiki page without having access the sql database.

astridm

Accurate Species TRee Reconstruction with Internode Distances

beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees

beast-mcmc-pisca

Beast-mcmc 1.8 commit 199fdb + PISCA. Compatible with MC3.

bladder_scripts

Scripts used to call variants for a pilot study on bladder cancer (intended for private usage)

breakclone

broadsims

Scripts used to conduct simulations and analyze the results using SimPhy to conduct ILS-based species tree reconstruction methods

cellcoal

combdepth

Program to calculate the length of the genomic intersection of an arbitrary number of samples at different minimum depths

copykit

Toolkit for single-cell copy number analysis

dmalloweb.github.io

My personal webpage

gcp-docker

Docker Image for Globus Personal Connect Client

genomedepth

Small C program to efficiently generate summary statistics of sequencing depth and gap size. It uses the result of bedtools genomecov -bga -ibam as input.

goldencheetahaarch64

inkscape-guide-tools

Inkscape extensions related to guides : add grids, centered guides, margin guides

ithe

IntraTumor Heterogeneity Estimator

lviprojectdnascripts

Repository to replicate the DNA-seq and downstream analyses in: Characterization of the lymphovascular invasion microenvironment reveals immune response dichotomy. Rivero-Gutierrez, Mallo, et al. 2022

manuscriptscripts_dcisrecurrencevsprogression

Scripts to perform the data analysis in Fortunato, Mallo, Cisneros, et al. 2024

mithe

Multisample IntraTumor Heterogeneity Estimator

mpest1.5_mod

Modified version of Liu's MPEST 1.5

multi-locus-bootstrapping

Creates sets of bootstrap replicates for multi-locus bootstrapping

njstm

Modified version of NJst to better accommodate missing data

njstm_scripts

Simulation study of njstm

parse_docs_path

Scripts to parse pathology reports. Intended for personal use only

phydyn

PhyDyn: Epidemiological modelling in BEAST

phylip

Repository with Phylip 3.697 with binaries for Apple Silicon

pisca

ppipilot

Scripts used for a specific pilot project (intended for personal use only)

recphyloxml

PhyloXML inspired format to represent reconciliations

rwty

R We There Yet?