Alternatives and similar repositories for pysradb

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

• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆341Updated 10 months ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆297Updated 2 years ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆336Updated this week
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆313Updated 4 years ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated 3 weeks ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆252Updated 4 months ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆265Updated 2 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 11 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆212Updated 2 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆269Updated last year
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆227Updated this week
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆275Updated last year
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆218Updated 2 months ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆409Updated last year
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆307Updated 2 years ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆280Updated 11 months ago
• CompEpigen / figeno
  Tool for plotting sequencing data along genomic coordinates.
  ☆295Updated last month
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆254Updated 2 years ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆138Updated 10 years ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆474Updated 3 months ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 5 years ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆205Updated 3 weeks ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆242Updated 2 months ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆232Updated 5 months ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆148Updated 9 months ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆250Updated 6 months ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆168Updated last week
• vanheeringen-lab / seq2science
  Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workf…
  ☆162Updated last month
• usadellab / Trimmomatic
  ☆253Updated last year
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆234Updated 4 years ago