DrDxMe - Advanced Bioinformatics Tools for Molecular Diagnostics

DrDxMe Logo KillShot

*Contact Jason.Limberis@ucsf.edu for access.

Files are automatically deleted after 21 days. Very large files may be removed earlier.

How we got our name: ℞ (Rx) is shorthand for the latin "recipere" which translates to "to take" or "recipe". Dx comes from this and is shorthand for diagnosis. Thus, Doctor Diagnose Me or DrDx.Me.


Codebase Summary
HTML
10,000+ lines
JavaScript
7,500+ lines
R
6,000+ lines
Shell
5,000+ lines
Python
1,500+ lines
PHP
1,000+ lines
CSS
1,000+ lines
Total: ~32,000+ lines across ~730 files
nanoLN
Process Nanopore ligation assay data
nanoComb
Combine nanoLN data
Basecaller
Convert Nanopore fast5 files to fastq*
nanoUMI
Process Nanopore UMI assay data
primerJinn
Designs primers for a multiplex PCR
hissPCR primer designer
Design primers for use with hissPCR
stilPCR
Process stilPCR assay data
spotPCR
spotPCR alignments
URAdime
Targeted sequence dimer and superamplicon detection
DeeDee
Detect deletions from WGS of knockout mutants
RvAligner
Align Nanopore or Illumina fastq to H37Rv genome and summarize genes
WGS pipeline
Align Illumina fastq to genome and call mutations*
RNAseq pipeline
Align Illumina fastq to genome and call counts for RNAseq*
RiboSeq pipeline
Complete Ribosome profiling pipeline*
svTyper
Detect and characterize structural variants and insertion sequences
TBprofiler pipeline
Predict drug resistance for M. tuberculosis from whole genome sequencing*
blastOFF
Blast unaligned sequences from bam file and summarize
10X CovCalc
Calculate required sequencing reads for 10x Genomics experiments
SeqCalcs
Calculate the expected amplicon coverage in a sequencing run amongst other functions
subSampler
Fastq subsampler to 100mb for Deeplex webapp
perrp
Alignment summary for M. tuberculosis sputa samples
SinS
How much of an original sputum sample am I using in my test?
crack
Run Kraken2 on paired fastq*
Oscar
Opentrons protocols
PubMed Prolific
PubMed Prolific PI search
WorldGS
Mutation prevelances in genes in global M. tuberculosis collection
c0unt
Automated CFU counter
count4U
CFU qPCR
PaperPusherAI
Comprehensive AI generated table of current litrature based on search terms
WHO TB Catalog
Interactive visualization of WHO TB mutation catalog for drug resistance
TBProfilerView
Interactive visualization of TB Profiler analysis results
gUNITS
Common biology calculations and conversions
DNAviz
An simple interactive DNA/RNA sequence visualization tool
PoP
Publish or perish pong
BB
Bacilli Blaster: Kill 'em all
PacManLung
A rip-off of pacman just for laughs
ScienceBuff
Workout planner
MC
Calculate the cost of meetings based on attendee salaries