si-medbif Goto Github PK

ai-md-variant-calling

Sequence analysis pipelines

batmansing

Singularity image for BATMAN R-package

bdm_workflow

A collection of workflows

chihuahua_genome

Scripts for supporting genome assembly of a Chihuahua

configfiles

Examples of files for configuring various software, e.g. vim, tmux.

deepfocus

deeppath

Classification of Lung cancer slide images using deep-learning

deeppost

Deep leaning project to identify prostate cancer in biopsy slides (.svs) file. Codes were inspired by ncoudrey's DeepPATH project but within new coding for complying with Tensorflow 2.0

dengue_dx_ai

Repository for R scripts for Dengue Prognosis Project

dengue_foci

A project aims to count numbers and measure areas of dengue foci from focus forming assay (FFA), 2021.

exomeseq

Analysing sequence data from whole exome sequencing or targeted gene panel sequencing.

fastfastqtransfer

git-workshop

idap

Integrative Database and Analytics Platform for Cancer Precision Medicine

idap-azkaban-jobs

A set of NGS data analysis pipeline 👨‍💻

jupyter-openslide-tflearn

Singularity container for jupyter notebook with deep learning and image processing modules

markdown-texts

Template for a blog hosted on GitHub Pages

medbif2021

Faculty of Medicine Siriraj Hospital, Mahidol UniversityMedical Bioinformatics Class 2021 Resume

medbif2022

Roster of Medical Bioinformatics Class 2022

neoantigens

Wrappers for software to identify tumor neoantigens

pathscan

An easy to use tool to identify pathogenic variants in genomic data; identifies variants listed as pathogenic in ClinVar that the ACMG recommendation implies should be incidental, reportable findings from VCFs, Complete Genomics variant files, and 23andMe SNP reports.

python-plot

Scripts for plotting various data sets using Python.

redcap-docker-compose

A docker-compose script for building REDCap with Mailhog

redcap_zkv

REDCap Data dictionary for Zika Virus and CNS Anomaly project

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

si-health

singularity_def

repository for singularity definition file

sire503_2018

SIRE503 Course

sire504

Datafiles and presentations used in "SIRE504 Introduction to programming with Python"