ShahCompBio

All

139 repositories

nanoseq
Public
Nanopore demultiplexing, QC and alignment pipeline
Nextflow
•
MIT License
•83•0•0•0•Updated Feb 21, 2025Feb 21, 2025
igver
Public
Automatically take IGV snapshots
automation bioinformatics igv bioinformatics-tool
Python
•
MIT License
•0•1•0•0•Updated Feb 20, 2025Feb 20, 2025
proteomegenerator-smk
Public
Snakemake workflow for proteomegenerator Isabl app
Python
•
MIT License
•0•0•0•0•Updated Feb 17, 2025Feb 17, 2025
transdecoder-smk
Public
snakemake pipeline for transdecoder
Python
•
MIT License
•0•0•0•0•Updated Feb 17, 2025Feb 17, 2025
bambu-smk
Public
Snakemake workflow for transcript assembly with Bambu
R
•
MIT License
•0•0•0•0•Updated Feb 14, 2025Feb 14, 2025
driver-concordance
Public
A pipeline to process CN and VCF data between paired samples to calculate driver event concordance
Python
•0•0•0•0•Updated Feb 14, 2025Feb 14, 2025
rustbam
Public
Rust-powered BAM depth extraction with Python bindings
rust bioinformatics genomics bam pyo3
Rust
•
MIT License
•0•0•0•0•Updated Feb 10, 2025Feb 10, 2025
SVChordinator
Public
merge, annotate and visualize structural variants
Python
•
Apache License 2.0
•0•0•0•0•Updated Jan 28, 2025Jan 28, 2025
hairloom
Public
A tool for analyzing split reads (focusing on long-read data)
bioinformatics nanopore genomics
Python
•
MIT License
•0•0•0•0•Updated Jan 27, 2025Jan 27, 2025
ontmont
Public
ONT split read analysis
Python
•
MIT License
•0•1•0•0•Updated Jan 16, 2025Jan 16, 2025
signals
Public
Single Cell Genomes with Allele Specificity
bioinformatics rna-seq single-cell
R
•
Other
•1•8•1•0•Updated Jan 7, 2025Jan 7, 2025
alhena_igo
Public
Alhena loader for IGO
Python
•
MIT License
•0•0•0•1•Updated Dec 20, 2024Dec 20, 2024
gdan-sv-consensus
Public
Getting GDAN SV consensus based on bedpe files
Python
•0•1•0•0•Updated Dec 10, 2024Dec 10, 2024
wgs_analysis
Public
Python
•1•1•0•1•Updated Nov 27, 2024Nov 27, 2024
scrna_demultiplexing
Public
Python
•
MIT License
•1•4•0•0•Updated Nov 18, 2024Nov 18, 2024
cellranger_utils
Public
Python
•
GNU General Public License v3.0
•1•0•0•0•Updated Nov 18, 2024Nov 18, 2024
doubleTime
Public
doubleTime is a method to estimate the timing of whole-genome doubling event(s) on a clone tree using SNVs
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Nov 15, 2024Nov 15, 2024
wgs
Public
Whole genome workflows
Python
•6•12•0•0•Updated Nov 9, 2024Nov 9, 2024
pypeliner
Public
Python
•
GNU General Public License v3.0
•5•2•0•0•Updated Oct 16, 2024Oct 16, 2024
alhenaloader
Public
Python
•
MIT License
•0•0•0•1•Updated Sep 26, 2024Sep 26, 2024
scdna_replication_paper
Public
Investigating DNA replication dynamics using DLP data
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Jul 31, 2024Jul 31, 2024
scdna_replication_tools
Public
Tools for assigning S-phase cells to clones and inferring single-cell replication timing (scRT) profiles
Jupyter Notebook
•
MIT License
•1•1•1•0•Updated Jul 29, 2024Jul 29, 2024
medicc2_nextflow
Public
Medicc2 nextflow pipeline
Nextflow
•1•1•0•2•Updated Jul 25, 2024Jul 25, 2024
bulk-illumina-rnaseq
Public
RNA seq analysis pipeline for alignment and quantification of bulk illumina data
Nextflow
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MIT License
•721•0•0•0•Updated Jun 29, 2024Jun 29, 2024
generate_mafs
Public
Generate Variant Tables from Isabl Results
Python
•1•0•0•0•Updated Jun 27, 2024Jun 27, 2024
oncokb-annotation
Public
Simple script to annotate variants using oncokb
Shell
•0•0•0•0•Updated May 31, 2024May 31, 2024
onboarding
Public
1•1•0•0•Updated Apr 15, 2024Apr 15, 2024
scgenome-deprecated
Public
Jupyter Notebook
•4•3•6•9•Updated Mar 28, 2024Mar 28, 2024
savana-pipeline
Public
SAVANA SV caller pipeline: https://github.com/cortes-ciriano-lab/savana
Python
•0•0•0•0•Updated Feb 23, 2024Feb 23, 2024
drost-rhabdoids
Public
Analysis of rhabdoid ONT WGS samples from Drost lab
Python
•0•0•0•0•Updated Jan 18, 2024Jan 18, 2024