6 results found Sort:

saketkc
pysradb saketkc
52
315
bsd-3-clause
13
Package for fetching metadata and downloading data from SRA/ENA/GEO
ena sra ncbi-sra sratoolkit bioinformatics ncbi-sra-archive bioinformatics-pipeline
Created 2018-11-29
660 commits to develop branch, last one about a month ago
wwood
kingfisher-download wwood
38
250
gpl-3.0
7
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
sra fastq-files aspera-client
Created 2019-07-28
228 commits to main branch, last one 5 months ago
vanheeringen-lab
seq2science vanheeringen-lab
27
156
mit
6
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
ngs sra fastq rna-seq atac-seq chip-seq pipeline snakemake workflows bioinformatics reproducible-research bioinformatics-pipeline
Created 2019-07-11
1,483 commits to master branch, last one 10 months ago
nf-core
fetchngs nf-core
74
154
mit
100
Pipeline to fetch metadata and raw FastQ files from public databases
ena geo sra ddbj fastq nf-core synapse download nextflow pipeline workflow
Created 2021-06-03
1,079 commits to master branch, last one 9 months ago
BioOmics
iSeq BioOmics
10
136
mit
1
Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
ebi gsa ngs sra axel ddbj wget aspera metadata bioinformatics
Created 2024-05-05
134 commits to main branch, last one 4 days ago
showteeth
scfetch showteeth
4
34
gpl-3.0
2
Access and Format Single-cell RNA-seq Datasets from Public Resources
bam geo sra fastq zenodo cellxgene panglaodb human-cell-atlas ucsc-cell-browser single-cell-rna-seq format-conversion-tool
Created 2023-07-12
92 commits to main branch, last one about a month ago