Alternatives and similar repositories for cufflinks

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

• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆440Updated last year
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆264Updated 2 years ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆435Updated this week
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆720Updated 2 weeks ago
• STAR-Fusion / STAR-Fusion
  STAR-Fusion codebase
  ☆240Updated last week
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆241Updated 2 years ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆316Updated 2 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆541Updated 10 months ago
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆312Updated 2 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆288Updated 7 months ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆411Updated 4 months ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆292Updated 2 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆265Updated last year
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆737Updated last month
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆424Updated 10 months ago
• pachterlab / sleuth
  Differential analysis of RNA-Seq
  ☆304Updated 10 months ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆339Updated 9 months ago
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆326Updated 2 years ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆463Updated 2 weeks ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆386Updated 5 months ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆395Updated this week
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆317Updated 11 months ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆591Updated last month
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆501Updated 6 months ago
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆209Updated 5 years ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆419Updated 3 weeks ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆806Updated 10 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆238Updated last month
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆428Updated last year