Alternatives and similar repositories for sge

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

• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆99Updated last year
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆115Updated last month
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆72Updated 10 months ago
• bmvdgeijn / WASP
  WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
  ☆110Updated 4 years ago
• francois-a / fastqtl
  Enhanced version of the FastQTL QTL mapper
  ☆71Updated 2 years ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆73Updated last year
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆29Updated 2 weeks ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆82Updated 10 months ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆61Updated 2 months ago
• epi2me-labs / wf-single-cell
  ☆98Updated last month
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆120Updated last month
• ivanek / Gviz
  This is the Gviz development repository. Gviz plots data and annotation information along genomic coordinates.
  ☆88Updated 10 months ago
• adamewing / tebreak
  Find and characterise transposable element insertions
  ☆20Updated 2 years ago
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆39Updated 2 weeks ago
• williamritchie / IRFinder
  Detecting intron retention from RNA-Seq experiments
  ☆55Updated last year
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆67Updated 6 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆60Updated 4 years ago
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆76Updated last year
• eQTL-Catalogue / qtlmap
  Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue
  ☆56Updated last month
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆113Updated 4 years ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆41Updated 3 years ago
• LuyiTian / FLAMES
  Full-length transcriptome splicing and mutation analysis
  ☆84Updated last year
• ucagenomix / sicelore
  Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…
  ☆78Updated 2 years ago
• noush-joglekar / scisorseqr
  scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two cond…
  ☆43Updated 2 years ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆63Updated 6 months ago
• snakemake-workflows / rna-seq-kallisto-sleuth
  A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
  ☆68Updated 3 weeks ago
• parklab / ShatterSeek
  ☆72Updated 2 years ago
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆67Updated 5 years ago
• Henikoff / Cut-and-Run
  ☆32Updated 7 years ago
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆117Updated 3 weeks ago