Alternatives and similar repositories for mirdeep2

Users that are interested in mirdeep2 are comparing it to the libraries listed below

• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆219Updated last month
• Xinglab / rmats2sashimiplot
  ☆149Updated 3 months ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆138Updated 5 years ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆125Updated 2 years ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆236Updated 3 weeks ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆239Updated last month
• ENCODE-DCC / rna-seq-pipeline
  ☆154Updated 2 years ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• nloyfer / wgbs_tools
  tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
  ☆166Updated 3 months ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 4 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆162Updated 2 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆245Updated this week
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆166Updated last year
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆170Updated 2 weeks ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆192Updated this week
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆216Updated last week
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆135Updated 2 years ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆134Updated this week
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆219Updated last month
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆258Updated 6 months ago
• ShujiaHuang / ilus
  A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysi…
  ☆138Updated 3 months ago
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆159Updated this week
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆141Updated 2 years ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆90Updated last month
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆106Updated 2 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆216Updated last month
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆152Updated last year
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆223Updated 3 months 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
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆279Updated last year