bioThai's repositories
cutTag-pipeline-singularity
MaxsonBraun Lab pipeline for Cut&Tag analysis. Forked for containerization improvements.
Bulk-RNA-seq-pipeline-PE
Forked for Singularity containerization. Currently a work in progress.
slurm-snakemake-profile
Forked from @gartician to add a slurm profile for Singularity-containerized pipelines
motif-mark
Python scripts to identify and visualize sequence motifs based on sequences in a FASTA file and a given text file of motifs to search for.
Deduper-bioThai
Reference-based PCR duplicate removal tool. The deduplicator (deduper) Python script in this repository takes in SAM files of single-end RNA-seq reads and a text file of unique molecular identifiers (UMIs) to be used as a reference. The deduper script outputs a deduped SAM file and summary statistics about the output deduped SAM file.
Demultiplex
Script to demultiplex 52 FASTQ files that contain biological reads with incorrect indexes or unmatched/low-quality-score indexes. This algorithm figures out which reads have hopped indexes and which reads have unmatched/low quality indexes, and separates these reads from the correctly-indexed reads. Each correctly-indexed read is separated into different bins/files based on their indexes.
world_database_gui_java
A JavaFX GUI to retrieve and display data from a sample database. Implements event handlers and multi-threading to create/execute SQL queries and update visual control elements. Multi-threading is implemented via nested/inner classes, Task, and Runnable interfaces. Event handlers are implemented using lambda expressions.
Semester_course_rosters_java
Implements nested/two-dimensional ArrayLists, a selection sort algorithm, multiple classes, and inheritance. Reads/processes course info and student registration data from two given text files, and assigns students to certain course section rosters based on registration data.
bookstore_file_processing_java
A Java program that reads bookstore inventory data from two text files, algorithmically processes the data, and writes data into appropriate output files.
interest_calculator_py
Python program to calculate simple interest on a user-inputted loan amount.
linked_list_cpp
C++ exercise in using linked lists, pointers, and managing manually-inputted list items.
hello-world
Github intro exercise