Alternatives and similar repositories for nextflow_pipelines

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

• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆128Updated 3 years ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆145Updated 3 months ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆120Updated last month
• nf-core / differentialabundance
  Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
  ☆84Updated last week
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆173Updated last year
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆137Updated 2 years ago
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆107Updated 5 months ago
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆133Updated last year
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆152Updated last year
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆29Updated 3 weeks ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆115Updated last month
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆105Updated 4 years ago
• nf-core / hic
  Analysis of Chromosome Conformation Capture data (Hi-C)
  ☆102Updated last week
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆223Updated last week
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆117Updated 3 weeks ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆207Updated 2 months ago
• epi2me-labs / wf-single-cell
  ☆99Updated this week
• nf-core / fetchngs
  Pipeline to fetch metadata and raw FastQ files from public databases
  ☆183Updated last week
• adamewing / methylartist
  Tools for plotting methylation data in various ways
  ☆165Updated this week
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆153Updated 3 months ago
• davetang / learning_vcf_file
  Learning the Variant Call Format
  ☆147Updated 3 months ago
• getzlab / rnaseqc
  Fast, efficient RNA-Seq metrics for quality control and process optimization
  ☆175Updated last year
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆217Updated 4 months ago
• gagneurlab / drop
  Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
  ☆158Updated 2 weeks ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆244Updated last week
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆97Updated last week
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆154Updated last year
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆76Updated last year
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 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