402 skills found · Page 6 of 14
FreedomIntelligence / bio-crispr-screens-crispresso-editingCRISPResso2 for analyzing CRISPR gene editing outcomes. Quantifies indels, HDR efficiency, and generates comprehensive editing reports
FreedomIntelligence / bio-crispr-screens-hit-callingStatistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes
FreedomIntelligence / bio-crispr-screens-mageck-analysisMAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis. Covers count normalization, gene ranking, and pathway analysis
FreedomIntelligence / bio-crispr-screens-screen-qcQuality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and essential gene recovery
FreedomIntelligence / bio-ctdna-mutation-detectionDetects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-based error suppression. Reliably detects mutations at VAF above 0.5 percent using consensus-based approaches
FreedomIntelligence / bio-differential-splicingDetects differential alternative splicing between conditions using rMATS-turbo (BAM-based) or SUPPA2 diffSplice (TPM-based). Reports events with FDR-corrected significance and delta PSI effect sizes
FreedomIntelligence / bio-epidemiological-genomics-pathogen-typingPerform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA
FreedomIntelligence / bio-epidemiological-genomics-phylodynamicsConstruct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate divergence times, molecular clock rates, and ancestral states
FreedomIntelligence / bio-epidemiological-genomics-transmission-inferenceInfer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimate who-infected-whom from genomic and epidemiological data
FreedomIntelligence / bio-fragment-analysisAnalyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fragment ratios, and DELFI-style fragmentation profiles for cancer detection
FreedomIntelligence / bio-genome-engineering-base-editing-designDesign guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positions for C-to-T or A-to-G conversions without double-strand breaks
FreedomIntelligence / bio-genome-engineering-grna-designDesign guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local scoring algorithms. Score guides for on-target activity using Rule Set 2 and Azimuth models
FreedomIntelligence / bio-genome-engineering-hdr-template-designDesign homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates with optimized homology arms
FreedomIntelligence / bio-genome-engineering-off-target-predictionPredict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites genome-wide and assess guide specificity
FreedomIntelligence / bio-genome-engineering-prime-editing-designDesign pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer, PBS, and RT template sequences for precise genomic modifications without double-strand breaks
FreedomIntelligence / bio-hi-c-analysis-compartment-analysisDetect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices
FreedomIntelligence / bio-hi-c-analysis-contact-pairsProcess Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data
FreedomIntelligence / bio-hi-c-analysis-hic-data-ioLoad, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats
FreedomIntelligence / bio-hi-c-analysis-hic-differentialCompare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps
FreedomIntelligence / bio-hi-c-analysis-loop-callingDetect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify CTCF-mediated loops and enhancer-promoter contacts
FreedomIntelligence / bio-hi-c-analysis-matrix-operationsBalance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices
FreedomIntelligence / bio-imaging-mass-cytometry-data-preprocessingLoad and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization
FreedomIntelligence / bio-imaging-mass-cytometry-spatial-analysisSpatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing
FreedomIntelligence / bio-immunoinformatics-epitope-predictionPredict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. Identify immunogenic regions in antigens
FreedomIntelligence / bio-immunoinformatics-immunogenicity-scoringScore and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features. Rank candidates for vaccine design
FreedomIntelligence / bio-cfdna-preprocessingPreprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering
FreedomIntelligence / bio-alignment-pairwisePerform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner
FreedomIntelligence / bio-atac-seq-differential-accessibilityFind differentially accessible chromatin regions between conditions using DiffBind or DESeq2
FreedomIntelligence / bio-atac-seq-footprintingDetect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS
FreedomIntelligence / bio-compressed-filesRead and write compressed sequence files (gzip, bzip2, BGZF) using Biopython
