Package for fetching metadata and downloading data from SRA/ENA/GEO
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Feb 17, 2025 - Python
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ncbi-sra
Here are 18 public repositories matching this topic...
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
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Mar 30, 2020 - Python
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
python bioinformatics rna-seq conda bioinformatics-pipeline bioconda bioinformatics-analysis rna-seq-pipeline ncbi-sra rna-seq-workflows
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Jun 4, 2021 - Python
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
bioinformatics bioinformatics-pipeline phylogenetics orthology homology ncbi-sra gene-sequence-retrieval
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Apr 2, 2021 - Python
Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
bioinformatics-pipeline genbank ncbi-submission ncbi-genbank cdc sra ncbi-sra ncbi-biosamples gisaid gisaid-uploader biosample gisaid-format gisaid-upload seqsender ncird ncird-id cdc-influenza-division
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Feb 14, 2025 - Python
Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA
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Feb 29, 2024 - HTML
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Extract metadata from biosamples in NCBI
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Apr 12, 2021 - Python
A tool to prepare files and run/monitor programmatic submissions to NCBI
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Mar 5, 2024 - Python
fast utils for fetch and dump NCBI SRA archive raw data
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May 25, 2023 - Python
This Python script retrieve all children organism under an ancestor in NCBI taxonomy.
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Feb 19, 2025 - Python
Pulls Metadata from NCBI based on Sample name or SRR #
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Apr 27, 2021 - PowerShell
tair id to pubmed links for articls, genes, annotations, locus tag
pubmed genome-annotation ncbi genome-analysis ncbi-database tair topic-analysis ncbi-sra tair3 pubmed-literature literature-modelling
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Aug 21, 2024 - Python
Data and code used in the Plant Genomes dashboard
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Mar 13, 2022 - R
frequency of high level ranks in sequence databases
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Oct 27, 2024 - Python
The Docker integration for the r2g project.
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Aug 10, 2020 - Dockerfile
explore sra databases and sequence retrieval
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Aug 17, 2024 - Shell
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