Навыки: Разработка

Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-te...

Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefacti...

Delimits putative species boundaries from molecular data within the de Queiroz 2007 unified-lineage framework using ASAP...

Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword,...

Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or txi...

Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-r...

Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/d...

Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequence...

Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populati...

Defines cell populations in flow and spectral cytometry through manual gates (rectangle, polygon, quadrant, boolean) and...

Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and fin...

Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (...

Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species v...

Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Ca...

Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (l...

Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the...

Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with bedt...

Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) w...

Computes and interprets sequencing read depth and coverage over a genome, windows, or target regions with mosdepth (wind...

Performs set operations on genomic intervals - intersect (-wa/-wb/-wo/-wao/-loj/-c/-v/-u), subtract (-A), merge (-d, -c/...

Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest...

Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when findi...

Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-nor...

Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using coo...

Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregate...

Balances Hi-C contact matrices (ICE via cooler.balance_cooler, KR/SCALE/VC context), computes distance-decay expected wi...

Segment single cells from multiplexed IMC/MIBI tissue images using Mesmer/DeepCell, Cellpose, or ilastik+CellProfiler, c...

Quality control for IMC/MIBI data across pixel, channel, image, slide, and batch levels, covering Poisson-count SNR (cel...

Phases small variants, SVs, and methylation from Oxford Nanopore and PacBio long reads (read-backed/physical phasing) wi...

Designs and validates quantitative targeted metabolomics assays (MRM/SRM on triple-quadrupole, PRM on high-resolution in...

Detects cancer and infers tissue-of-origin from cfDNA methylation by choosing conversion chemistry (bisulfite vs EM-seq...

Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample di...

Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomi...

Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clus...

Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and...

Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding...

Frames the phasing/imputation pipeline before any tool runs: phasing and imputation are one Li-Stephens copying HMM (rec...

Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling,...

Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify hap...

Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics. Calculate pop...

Protein grouping and inference from peptide identifications. Use when resolving protein ambiguity from shared peptides....

Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too hi...

Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice ju...

Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Il...

Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove...

Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter conte...

Count reads per gene from aligned BAM files using Subread featureCounts. Use when processing BAM files from STAR/HISAT2...

Predicts RNA secondary structures using minimum free energy folding and partition function analysis with ViennaRNA (RNAf...