SCBIR Lab

All

24 repositories

nf-sbrnaseq
Public
Nextflow pipeline to process demultiplexed Illumina paired-end FASTQ files from multiple bacterial samples into a gene x cell count table.
Nextflow
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MIT License
•0•0•0•0•Updated Dec 11, 2024Dec 11, 2024
hts-tools
Public
🏮 Parsing and analysing platereader absorbance and fluorescence data.
data-analysis fluorescence high-throughput platereader high-throughput-screening assay-analysis
Python
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MIT License
•0•0•3•0•Updated Nov 12, 2024Nov 12, 2024
schemist
Public
⬢⬢⬢ Organizing and processing tables of chemical structures.
chemistry cheminformatics smiles selfies smiles-strings
Python
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MIT License
•0•0•0•0•Updated Oct 28, 2024Oct 28, 2024
nf-crispriseq
Public
Calculate fitness from massive competition experiments using CRISPRi-seq.
Nextflow
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MIT License
•0•0•0•0•Updated Oct 23, 2024Oct 23, 2024
crispio
Public
🌱 Designing CRISPRi experiments in bacteria
bioinformatics fitness crispr bacteria bacterial-genomes guide-rna-library crispri
Python
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MIT License
•0•0•0•0•Updated Oct 14, 2024Oct 14, 2024
nf-platereader-screen
Public
Process files from Biotek platereaders, normalise output, perform QC, make plots, and do statistical tests.
Nextflow
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MIT License
•0•0•0•0•Updated Oct 6, 2024Oct 6, 2024
carabiner
Public
🪨 Useful python utilities.
utilities utilities-python
Python
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MIT License
•0•0•0•0•Updated Oct 5, 2024Oct 5, 2024
abx-disco-dynamo
Public
Interface to demonstrate Figure 1 from https://doi.org/10.1042/BCJ20220062
Python
•0•0•0•0•Updated Sep 27, 2024Sep 27, 2024
nf-ggi
Public
Predict gene-gene interactions based on protein-protein interaction predictions and similar metabolites.
Nextflow
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MIT License
•0•0•0•0•Updated Sep 22, 2024Sep 22, 2024
yunta
Public
🍐 Predicting protein-protein interactions and structures from multiple sequence alignments.
Python
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Other
•17•0•0•0•Updated Sep 22, 2024Sep 22, 2024
rf2t-micro
Public
🌹 RosettaFold-2track command-line interface.
Python
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MIT License
•442•0•0•0•Updated Sep 22, 2024Sep 22, 2024
nf-ont-call-variants
Public
Nextflow pipeline to call variants from Nanopore FASTQ files from bacterial clones relative to a wildtype control.
Nextflow
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MIT License
•0•0•0•0•Updated Jul 21, 2024Jul 21, 2024
envs
Public
Conda environment definition files for making environments that are useful for various analysis tasks
MIT License
•0•0•0•0•Updated Jul 5, 2024Jul 5, 2024
2024-Parkhill-BiochemJ
Public
Integrating bacterial molecular genetics with chemical biology for renewed antibacterial drug discovery: Jupyter notebook and data.
publications drug-discovery antibiotics publication-code
Jupyter Notebook
•0•0•0•0•Updated Jul 4, 2024Jul 4, 2024
.github
Public
Public profile repo
0•0•0•0•Updated Jun 20, 2024Jun 20, 2024
nf-inspect
Public
🧬🔍 Nextflow pipeline to process demultiplexed Illumina paired-end FASTQ files from INSPECT experiments.
Nextflow
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MIT License
•0•0•0•0•Updated Jun 5, 2024Jun 5, 2024
RF2-Lite
Public
Python
•5•0•0•0•Updated Jun 1, 2024Jun 1, 2024
bioino
Public
💻 Interconverting FASTA, GFF, and CSV.
bioinformatics gff3 sequencing fasta gff
Python
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MIT License
•0•0•0•0•Updated Mar 19, 2024Mar 19, 2024
monte-barcode
Public
🔴🟢🔵⚫️ Generating sets of random DNA sequences optimized for use in high-throughput sequencing.
ngs sequencing barcode barcode-generator dna illumina molecular-biology
Python
•
MIT License
•0•0•0•0•Updated Jul 20, 2023Jul 20, 2023
scbirlab.github.io
Public
Lab website
Python
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MIT License
•0•0•0•0•Updated Jul 4, 2023Jul 4, 2023
nf-ont-sbrnaseq
Public
Nextflow pipeline to process Nanopore POD5 files from multiple bacterial samples into a gene x cell count table
Nextflow
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MIT License
•0•0•0•0•Updated Jul 1, 2023Jul 1, 2023
ogilo
Public
⛓️ Automating construction of oligo library sequences for oligo array synthesis.
synthetic-biology crispr molecular-biology oligonucleotide crispr-design oligo-design
Python
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MIT License
•0•0•0•0•Updated Jun 28, 2023Jun 28, 2023
streq
Public
🧬 Python utilities for working with nucleotide sequence strings.
biology sequencing dna rna sequence molecular-biology nucleotides
Python
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MIT License
•0•0•1•0•Updated Jun 2, 2023Jun 2, 2023
nemony
Public
🧠 Deterministically encode text as mnemonic adjective-noun pairs.
hashing mnemonic mnemonic-generator
Python
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MIT License
•0•1•0•0•Updated Jun 2, 2023Jun 2, 2023