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SkillsMP hat 207 Skills aus jaechang-hits/SciAgent-Skills gesammelt. Öffne einen Skill, um Quelle und Details zu prüfen.
jaechang-hits/SciAgent-SkillsEs werden 40 von 207 gesammelten Skills angezeigt.
Interactive viewer for microscopy. Displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, Tracks layers; supports annotation, plugin analysis, headless screenshots. Core visualization for Python bioimage workflows. Use ImageJ/FIJI for macro processing;…
Quellsprache: Englisch
Computer vision for bio-image preprocessing, feature detection, real-time microscopy. Color conversion, morphology, contour/blob detection, template matching, optical flow on fluorescence/brightfield. 10-100× faster than pure Python via C++. Use scikit-image…
Quellsprache: Englisch
Python bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops. Automates Fiji headlessly from Python. Use scikit-image for pure Python without Fiji plugins; napari for…
Quellsprache: Englisch
Python image processing for microscopy and bioimage analysis. Read/write images, filter (Gaussian, median, LoG), segment (thresholding, watershed, active contours), measure region properties, detect features. SciPy/NumPy ecosystem. Use OpenCV for real-time…
Quellsprache: Englisch
Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm. Locate particles (fluorescent spots, colloids, vesicles, cells) per frame, link into trajectories, filter short tracks, and compute MSD for diffusion…
Quellsprache: Englisch
Interactive scientific visualization with Plotly. Two APIs: plotly.express (px) for one-liner DataFrame plots, plotly.graph_objects (go) for trace-level control. 40+ chart types with hover, zoom, pan, animation. Exports HTML or static PNG/SVG/PDF via kaleido.…
Quellsprache: Englisch
Guide for choosing and creating scientific visualizations for publications and talks. Covers chart-type selection by data structure, color theory for accessibility/print, figure composition, journal formatting (Nature, Cell, ACS), and common pitfalls. Consult…
Quellsprache: Englisch
Guide for annotating statistical significance (p-value asterisks) on comparison plots. Covers standard notation (ns, *, **, ***, ****), matplotlib bracket+asterisk implementation, and use with seaborn box/violin/bar plots. Use when preparing publication-ready…
Quellsprache: Englisch
GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). Load matrix, filter by TFs, infer TF-target-importance links, save network. Dask-parallelized to single-cell scale. Core SCENIC component.
Quellsprache: Englisch
Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. Use for batch processing, custom pipelines, format conversion, PubMed/GenBank queries. For quick gene…
Quellsprache: Englisch
Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic trees (Phylo). Use for gene family studies, phylogenomics,…
Quellsprache: Englisch
ETE Toolkit (ETE3): Python phylogenetic tree analysis and visualization. Parse Newick/NHX/PhyloXML, traverse/annotate nodes, render figures with TreeStyle/NodeStyle, integrate NCBI taxonomy, run PhyloTree comparative genomics. Use for species trees, gene…
Quellsprache: Englisch
De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER. findMotifsGenome.pl finds over-represented patterns vs background; annotatePeaks.pl assigns context (TSS distance, gene, repeat). Use after MACS3 to identify enriched TFs, annotate…
Quellsprache: Englisch
Poisson-model peak caller for ChIP-seq/ATAC-seq BAMs. MACS3 callpeak finds enriched regions (TF sites or histone marks) vs input/IgG; outputs BED narrowPeak/broadPeak for motif analysis, annotation, and differential binding. Use narrow peaks for TF ChIP-seq…
Quellsprache: Englisch
Python library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees (NJ, UPGMA), diversity (Shannon, Faith PD, Bray-Curtis, UniFrac), ordination (PCoA, CCA, RDA), stats (PERMANOVA, ANOSIM, Mantel), file I/O…
Quellsprache: Englisch
Python API v2 for Opentrons OT-2/Flex liquid handlers: protocols as Python files with metadata and run(); control pipettes, labware, and modules (thermocycler, heater-shaker, magnetic, temperature). Simulate via opentrons_simulate then upload. Use PyLabRobot…
Quellsprache: Englisch
Hardware-agnostic Python liquid-handler library: portable scripts run on Hamilton STAR, Tecan Freedom EVO, Opentrons OT-2, or a simulator without vendor lock-in. For protocol automation, method dev, plate reformatting, serial dilutions, and Python lab…
Quellsprache: Englisch
Auto-annotate plasmids with features (promoters, terminators, resistance, origins, tags, fluorescent proteins) via BLAST against curated DBs (Addgene, fpbase, SnapGene). FASTA or raw sequence in; annotated GenBank, interactive HTML maps, CSV tables out.…
Quellsprache: Englisch
Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings. Pipeline: sequence → MFE → partition function and pair-probability matrix → dot-bracket → duplex. Use for siRNA/sgRNA targeting,…
Quellsprache: Englisch
API + Python SDK for ordering cell-free protein expression and binding assays. Submit sequences for expression (10–100 µg), measure binding affinity (KD) against targets, track status, and retrieve results programmatically — no wet-lab setup. Built for…
Quellsprache: Englisch
Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping. No REST API — uses ~6 GB XML download. Use drugbank-database-access for drugs; pubchem-compound-search…
Quellsprache: Englisch
MS spectral matching and metabolite ID with matchms. Import spectra (mzML, MGF, MSP, JSON), filter/normalize peaks, score similarity (cosine, modified cosine, fingerprint), build reproducible pipelines, identify unknowns vs spectral libraries. Use pyopenms…
Quellsprache: Englisch
MaxQuant + Perseus proteomics pipeline: run MaxQuant for LFQ and SILAC; parse proteinGroups.txt in Python; filter contaminants/decoys; log2 + median-normalize; impute MNAR; t-test with FDR; volcano plot; GO/pathway enrichment. Use Proteome Discoverer for…
Quellsprache: Englisch
MS data processing with PyOpenMS for LC-MS/MS proteomics and metabolomics — mzML/mzXML I/O, signal processing (smoothing, peak picking, centroiding), feature detection/linking, peptide/protein ID with FDR, untargeted metabolomics. Use matchms for simple…
Quellsprache: Englisch
scikit-learn compatible Python toolkit for time series ML: classify, cluster, regress, segment, transform with 30+ algorithms (ROCKET, InceptionTime, KNN-DTW, HIVE-COTE, WEASEL). Handles panel, multivariate, and unequal-length series. Maintained successor to…
Quellsprache: Englisch
Core Python library for astronomy/astrophysics: units with dimensional analysis, celestial coordinate transforms (ICRS/Galactic/AltAz/FK5), FITS I/O, tables (FITS/HDF5/VOTable/CSV), cosmology (Planck18, distance/age), precise time (UTC/TAI/TT/TDB, Julian,…
Quellsprache: Englisch
Parallel/distributed computing for larger-than-RAM data. Components: DataFrames (parallel pandas), Arrays (parallel NumPy), Bags, Futures, Schedulers. Scales laptop to HPC cluster. For single-machine speed use polars; for out-of-core without cluster use vaex.
Quellsprache: Englisch
Methodology for exploratory data analysis on scientific files. Decision frameworks by data type (tabular, sequence, image, spectral, structural, omics), quality assessment, report generation, format detection across 200+ formats. Use when given a data file…
Quellsprache: Englisch
Geospatial vector analysis extending pandas. Read/write spatial formats (Shapefile, GeoJSON, GeoPackage, Parquet, PostGIS), CRS handling, geometric ops (buffer, simplify, centroid, affine), spatial analysis (joins, overlays, dissolve, clipping, distance),…
Quellsprache: Englisch
LLM-driven hypothesis generation/testing on tabular data. Three methods: HypoGeniC (data-driven), HypoRefine (literature+data), Union. Iterative refinement, Redis caching, multi-hypothesis inference. Manual: hypothesis-generation; ideation:…
Quellsprache: Englisch
MATLAB/GNU Octave numerical computing: matrices, linear algebra, ODEs, signal processing, optimization, statistics, scientific visualization. MATLAB-syntax examples run on both. For Python use numpy/scipy; for statistical modeling use statsmodels.
Quellsprache: Englisch
Python toolkit for neurophysiological signal processing: ECG (HR, HRV, R-peaks), EEG (complexity, PSD), EMG (activation onset), EDA/GSR (SCR decomposition), PPG, and RSP. Includes synthetic signal simulation. Alternatives: BioSPPy (less maintained), MNE…
Quellsprache: Englisch
Pipeline for Neuropixels extracellular electrophysiology: probe geometry (ProbeInterface), Kilosort sorting via SpikeInterface, quality metrics, unit curation (ISI, firing rate, SNR), post-sort analysis (PSTH, tuning curves, population decoding). Supports…
Quellsprache: Englisch
Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure), or Kubernetes via a single config change. Powers nf-core. Use Snakemake for…
Quellsprache: Englisch
Fast in-memory DataFrame with lazy evaluation, parallel execution, Arrow backend. Use for tabular data in RAM (1–100 GB) when pandas is too slow. Expression API: select, filter, group_by, joins, pivots, window. Lazy mode enables predicate/projection pushdown.…
Quellsprache: Englisch
Python Materials Genomics library for structure analysis, thermodynamics, and electronic properties. Parse/create crystal structures (CIF, POSCAR), query Materials Project for DFT-computed properties, analyze phase and Pourbaix diagrams, compute XRD patterns,…
Quellsprache: Englisch
Python framework for single- and multi-objective optimization with evolutionary algorithms. Define vectorized objectives and constraints; solve with NSGA-II, NSGA-III, MOEA/D, GAs, or differential evolution. Analyze Pareto fronts, visualize trade-offs,…
Quellsprache: Englisch
Process-based discrete-event simulation. Model queues, shared resources, timed events: manufacturing, service ops, network traffic, logistics. Processes are Python generators yielding events. Resources: capacity-limited (Resource/Priority/Preemptive), bulk…
Quellsprache: Englisch
Python-based workflow manager for reproducible, scalable pipelines. Define rules with file-based dependencies; Snakemake resolves execution order and parallelism. Runs local, SLURM, LSF, AWS, GCP via profiles; per-rule conda/Singularity envs. For NGS…
Quellsprache: Englisch
Unified Python framework for extracellular electrophysiology. Load 20+ formats (SpikeGLX, OpenEphys, NWB, Intan, Maxwell, Blackrock), preprocess, run 10+ sorters (Kilosort4, SpykingCircus2, Tridesclous, MountainSort5) via one API, compute quality metrics…
Quellsprache: Englisch