Package for fetching metadata and downloading data from SRA/ENA/GEO
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Oct 25, 2024 - Python
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sratoolkit
Here are 12 public repositories matching this topic...
GEO RNA-seq Experiments Processing Pipeline
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Oct 25, 2019 - R
dockerfile bioinformatics r docker-image fair bioinformatics-data bioinformatics-databases sra-files rpackage sratoolkit bioinformatics-tool dbgap
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Jul 26, 2019 - Jupyter Notebook
fast utils for fetch and dump NCBI SRA archive raw data
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May 25, 2023 - Python
Download Raw Reads from SRA Archive
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Feb 8, 2018 - Nextflow
Decrypt the encrypted genome data files using SRA Toolkit
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Apr 6, 2019
RNA-seq code with Bowtie alignment and generating strain-specific counts using Emase
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Apr 4, 2022 - HTML
A reproducible RNA-Seq analysis pipeline for Staphylococcus aureus under antibiotic stress, utilizing Nextflow and Singularity. It involves genome mapping, read counting, and statistical analysis to identify differentially expressed genes (DEGs) and generates key visualizations.
shell bash cli r ubuntu nextflow hpc deseq2 google-cloud-platform samtools featurecounts bowtie ngs-analysis cutadapt ngs-pipeline fastqc sratoolkit apptainer
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Dec 9, 2024 - R
RNA-seq analysis from FASTQ to differential gene-expression using open-source tools
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Nov 19, 2024 - Jupyter Notebook
PARMIK is a fast and memory-efficient tool for identifying the "Partial Match" region between two genomic sequences.
smith-waterman k-mer k-mer-frequency k-mer-hashing genome-analysis bwa-mem metagenomic-analysis blastn sratoolkit genome-alignment dna-processing environment-sampling
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Oct 18, 2024 - C++
explore sra databases and sequence retrieval
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Aug 17, 2024 - Shell
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