Search Skills

bio-splicing-pipeline

Complete workflow from raw RNA-seq to differential splicing results. FASTQ → Read QC → STAR 2-pass → Junction QC → rMATS-turbo → Results → Visualizati...

by FreedomIntelligence

github 3 files

bio-splicing-quantification

Reference examples tested with: kallisto 0.50+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Python: p...

by FreedomIntelligence

github 3 files

bio-sra-data

Download raw sequencing data from the Sequence Read Archive using the SRA toolkit. brew install sratoolkit sudo apt install sra-toolkit conda install ...

by FreedomIntelligence

github 6 files

bio-structural-biology-alphafold-predictions

Reference examples tested with: BioPython 1.83+, matplotlib 3.8+, numpy 1.26+, scanpy 1.10+ Before using code patterns, verify installed versions matc...

by FreedomIntelligence

github 3 files

bio-structural-biology-modern-structure-prediction

Reference examples tested with: BioPython 1.83+, numpy 1.26+ Before using code patterns, verify installed versions match. If versions differ: Python: ...

by FreedomIntelligence

github 4 files

bio-substructure-search

Reference examples tested with: RDKit 2024.03+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <pack...

by FreedomIntelligence

github 3 files

bio-systems-biology-flux-balance-analysis

import cobra model = cobra.io.loadmodel('textbook') # E. coli core (95 reactions) model = cobra.io.loadmodel('iJO1366') # Full E. coli (2583 reacti...

by FreedomIntelligence

github 3 files

bio-systems-biology-gene-essentiality

import cobra from cobra.fluxanalysis import singlegenedeletion model = cobra.io.loadmodel('textbook') deletionresults = singlegenedeletion(model) esse...

by FreedomIntelligence

github 3 files

bio-systems-biology-metabolic-reconstruction

pip install carveme carve genome.faa -o model.xml carve genome.faa -o model.xml --format sbml carve genome.faa -o model.json --format json carve genom...

by FreedomIntelligence

github 3 files

bio-systems-biology-model-curation

pip install memote memote report snapshot model.xml --filename report.html memote run model.xml memote run --pytest-args "--tb=short" model.xml import...

by FreedomIntelligence

github 3 files

bio-tcr-bcr-analysis-immcantation-analysis

Reference examples tested with: MiXCR 4.6+, ggplot2 3.5+ Before using code patterns, verify installed versions match. If versions differ: R: packageVe...

by FreedomIntelligence

github 3 files

bio-tcr-bcr-analysis-repertoire-visualization

Reference examples tested with: MiXCR 4.6+, VDJtools 1.2.1+, ggplot2 3.5+, matplotlib 3.8+, pandas 2.2+, scanpy 1.10+, seaborn 0.13+ Before using code...

by FreedomIntelligence

github 3 files