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FreedomIntelligence / bio-clinical-databases-variant-prioritizationFilter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis
FreedomIntelligence / bio-clip-seq-clip-peak-callingPureCLIP uses an HMM to model crosslink sites, incorporating enrichment and truncation signals.
FreedomIntelligence / bio-codon-usageAnalyze codon usage patterns and calculate codon adaptation metrics using Biopython.
FreedomIntelligence / bio-compressed-filesRead and write compressed sequence files (gzip, bzip2, BGZF) using Biopython
FreedomIntelligence / bio-consensus-sequencesGenerate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus
FreedomIntelligence / bio-copy-number-cnv-annotationAnnotate CNVs with genes, pathways, and clinical significance
FreedomIntelligence / bio-crispr-screens-jacks-analysisJACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality
FreedomIntelligence / bio-data-visualization-circos-plotsCircular genome visualizations for displaying multiple data tracks around chromosome ideograms.
FreedomIntelligence / bio-entrez-fetchRetrieve records from NCBI databases using Biopython's Entrez module (EFetch, ESummary utilities).
FreedomIntelligence / bio-entrez-linkNavigate between NCBI databases using Biopython's Entrez module (ELink utility).
FreedomIntelligence / bio-entrez-searchSearch NCBI databases using Biopython's Entrez module (ESearch, EInfo, EGQuery utilities).
FreedomIntelligence / bio-filter-sequencesFilter and select sequences by criteria (length, ID, GC content, patterns) using Biopython
FreedomIntelligence / bio-flow-cytometry-compensation-transformationSpillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms
FreedomIntelligence / bio-flow-cytometry-differential-analysisDifferential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods
FreedomIntelligence / bio-flow-cytometry-fcs-handlingRead and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration
FreedomIntelligence / bio-flow-cytometry-gating-analysisManual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates
FreedomIntelligence / bio-genome-assembly-assembly-polishingImprove assembly accuracy by correcting errors using additional sequencing data.
FreedomIntelligence / bio-genome-assembly-assembly-qcEvaluate genome assembly quality with contiguity metrics (QUAST) and gene completeness (BUSCO).
FreedomIntelligence / bio-genome-assembly-long-read-assemblyAssemble genomes from Oxford Nanopore (ONT) or PacBio long reads for highly contiguous assemblies.
FreedomIntelligence / bio-genome-assembly-short-read-assemblyAssemble genomes from Illumina paired-end or single-end reads using SPAdes.
FreedomIntelligence / bio-genome-intervals-bed-file-basicsBED (Browser Extensible Data) format stores genomic intervals. Uses 0-based, half-open coordinates.
FreedomIntelligence / bio-genome-intervals-bigwig-tracksBigWig is an indexed binary format for continuous genomic data. Efficient for genome browsers and programmatic access.
FreedomIntelligence / bio-genome-intervals-coverage-analysisCalculate coverage and depth across genomic regions using bedtools and pybedtools.
FreedomIntelligence / bio-genome-intervals-gtf-gff-handlingGTF and GFF3 are standard gene annotation formats. Both use 1-based coordinates.
FreedomIntelligence / bio-genome-intervals-interval-arithmeticCore set operations on genomic intervals using bedtools (CLI) and pybedtools (Python).
FreedomIntelligence / bio-genome-intervals-proximity-operationsOperations for finding nearby features and extending intervals using bedtools and pybedtools.
FreedomIntelligence / bio-geo-dataQuery and access Gene Expression Omnibus datasets using Biopython's Entrez module.
FreedomIntelligence / bio-imaging-mass-cytometry-quality-metricsQuality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC
FreedomIntelligence / bio-isoform-switchingAnalyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain changes, NMD sensitivity, ORF alterations, and coding potential shifts between conditions
FreedomIntelligence / bio-liquid-biopsy-pipelineComplete workflow for cfDNA analysis from sequencing to clinical interpretation.
