pyrpipeReproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
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CellOCellO: Gene expression-based hierarchical cell type classification using the Cell Ontology
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slamdunkStreamlining SLAM-seq analysis with ultra-high sensitivity
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picardmetrics🚦 Run Picard on BAM files and collate 90 metrics into one file.
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gene-oracleFeature extraction algorithm for genomic data
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idealInteractive Differential Expression AnaLysis - DE made accessible and reproducible
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sample-sheetA permissively licensed library designed to replace Illumina's Experiment Manager
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dnaioRead and write FASTQ and FASTA efficiently from Python
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TeamTeriGenomics using open source tools, running on GCP or AWS
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unimapA EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
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rkmhClassify sequencing reads using MinHash.
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go4bioGolang for Bioinformatics
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GRAFIMOGRAph-based Finding of Individual Motif Occurrences
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wdlRunRElastic, reproducible, and reusable genomic data science tools from R backed by cloud resources
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PHATPathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
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CICEROCICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
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ntHashFast hash function for DNA sequences
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atroposAn NGS read trimming tool that is specific, sensitive, and speedy. (production)
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CeleScopeSingle Cell Analysis Pipelines
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simplesamSimple pure Python SAM parser and objects for working with SAM records
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dysgudysgu-SV is a collection of tools for calling structural variants using short or long reads
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quickExpa script for controlling expressions quickly in After Effects
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BridgeDbThe BridgeDb Library source code
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gnparserGNparser normalises scientific names and extracts their semantic elements.
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catchA package for designing compact and comprehensive capture probe sets.
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PrimerMinerR mased batch sequence downloader, with primer development and in silico evaluation capabilities
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tibannaTibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
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FEELncFEELnc : FlExible Extraction of LncRNA
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hotsubCommand line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources
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alevin-fry🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
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biolink-apiAPI for linked biological knowledge
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diffexprPorting DESeq2 and DEXSeq into python via rpy2
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squidSQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
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tftargets🎯 Human transcription factor target genes.
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nPhasePloidy agnostic phasing pipeline and algorithm
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