saketkc / pysradbLinks
Package for fetching metadata and downloading data from SRA/ENA/GEO
☆348Updated 2 weeks ago
Alternatives and similar repositories for pysradb
Users that are interested in pysradb are comparing it to the libraries listed below
Sorting:
- RNA-seq workflow using STAR and DESeq2☆351Updated last week
- parallel fastq-dump wrapper☆301Updated 2 years ago
- Customizable workflows based on snakemake and python for the analysis of NGS data☆395Updated last week
- Download FASTQ files from SRA or ENA repositories.☆353Updated 3 weeks ago
- Performant Pythonic GenomicRanges☆492Updated last month
- This Snakemake pipeline implements the GATK best-practices workflow☆262Updated 2 years ago
- A collection of scripts and notes related to genomics and bioinformatics☆217Updated 2 weeks ago
- Plot structural variant signals from many BAMs and CRAMs☆557Updated last year
- Miscellaneous collection of Python and R scripts for processing Iso-Seq data☆278Updated 2 years ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆447Updated last year
- Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.☆395Updated last month
- Tool for plotting sequencing data along genomic coordinates.☆335Updated 2 weeks ago
- Application for making ENCODE Blacklists☆333Updated 4 years ago
- Tool for the Quality Control of Long-Read Defined Transcriptomes☆250Updated 3 weeks ago
- Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.☆283Updated 4 months ago
- Web application to explore the Sequence Read Archive.☆218Updated 5 months ago
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆261Updated 5 months ago
- Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")☆328Updated 9 months ago
- SUPPA: Fast quantification of splicing and differential splicing☆290Updated last month
- Fast and accurate gene fusion detection from RNA-Seq data☆257Updated 3 months ago
- Nextflow training material☆207Updated this week
- Genome browser and variant annotation☆387Updated last month
- A tool to map bisulfite converted sequence reads and determine cytosine methylation states☆439Updated 4 months ago
- Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair☆184Updated last week
- GTEx & TOPMed data production and analysis pipelines☆390Updated 3 months ago
- A package for including transposable elements in differential enrichment analysis of sequencing datasets.☆273Updated last month
- A tool to find sequencing data and metadata from public databases.☆591Updated last year
- Documentation for the ANNOVAR software☆245Updated 4 months ago
- This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.☆245Updated 3 years ago
- Pipeline to fetch metadata and raw FastQ files from public databases☆184Updated last month