Alternatives and similar repositories for pysradb

Users that are interested in pysradb are comparing it to the libraries listed below

• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆299Updated 2 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆344Updated last year
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆396Updated 2 weeks ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆340Updated 2 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆216Updated last month
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆374Updated 2 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆257Updated 2 years ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆429Updated 8 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆483Updated 5 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆279Updated last year
• CompEpigen / figeno
  Tool for plotting sequencing data along genomic coordinates.
  ☆308Updated 2 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆273Updated last year
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆245Updated last week
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆236Updated this week
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆317Updated 4 years ago
• kcleal / gw
  Genome browser and variant annotation
  ☆369Updated 3 weeks ago
• pachterlab / ffq
  A tool to find sequencing data and metadata from public databases.
  ☆584Updated last year
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆243Updated 2 years ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆256Updated last month
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆234Updated this week
• vanheeringen-lab / genomepy
  genes and genomes at your fingertips
  ☆398Updated 3 months ago
• nextflow-io / training
  Nextflow training material
  ☆188Updated 2 weeks ago
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆322Updated 5 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆259Updated 6 months ago
• Xinglab / rmats-turbo
  ☆272Updated 9 months ago
• wwood / kingfisher-download
  Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
  ☆274Updated last week
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆244Updated 3 weeks ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆219Updated last month