bioThai

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.

Bulk-RNA-seq-pipeline-PE

Forked for Singularity containerization. Currently a work in progress.

cutTag-pipeline-singularity

MaxsonBraun Lab pipeline for Cut&Tag analysis. Forked for containerization improvements.

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.

gg_site

JavaScript/HTML/CSS. Fictitious site containing JavaScript games. Uses JavaScript to implement mobile menu, cookies to set light/dark mode, closure functions, and more.

git_exercise

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.

CITEViz

CITEViz: Replicating the Interactive Flow Cytometry Workflow in CITE-Seq

cutTag-pipeline

Pipeline for Cut&Tag analysis

bioThai/gg_site

JavaScript/HTML/CSS. Fictitious site containing JavaScript games. Uses JavaScript to implement mobile menu, cookies to set light/dark mode, closure functions, and more.

bioThai/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.

bioThai/Bulk-RNA-seq-pipeline-PE

Forked for Singularity containerization. Currently a work in progress.

bioThai/cutTag-pipeline-singularity

MaxsonBraun Lab pipeline for Cut&Tag analysis. Forked for containerization improvements.

bioThai/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.

bioThai/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.

bioThai/git_exercise

bioThai/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.

bioThai/hello-world

Github intro exercise

bioThai/interest_calculator_py

Python program to calculate simple interest on a user-inputted loan amount.

bioThai/linked_list_cpp

C++ exercise in using linked lists, pointers, and managing manually-inputted list items.

bioThai/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.

bioThai/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.

bioThai/slurm-snakemake-profile

Forked from @gartician to add a slurm profile for Singularity-containerized pipelines