Alternatives and similar repositories for SalmonTE:

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

• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆38Updated 3 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆56Updated 4 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 3 months ago
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆24Updated 2 weeks ago
• eQTL-Catalogue / qtlmap
  Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue
  ☆46Updated last week
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆108Updated 2 weeks ago
• parklab / ShatterSeek
  ☆66Updated last year
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆80Updated 3 weeks ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆111Updated 2 years ago
• kundajelab / phantompeakqualtools
  This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…
  ☆56Updated 4 years ago
• snystrom / memes
  An R interface to the MEME Suite
  ☆49Updated 4 months ago
• sirselim / illumina450k_filtering
  A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays
  ☆30Updated last year
• snakemake-workflows / rna-seq-kallisto-sleuth
  A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
  ☆66Updated this week
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 5 years ago
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆32Updated 2 years ago
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆66Updated 5 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆54Updated this week
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆54Updated 2 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆67Updated last month
• gagneurlab / OUTRIDER
  OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
  ☆49Updated this week
• MonashBioinformaticsPlatform / RSeQC
  fork of RSeQC python RNAseq metrics suit of tools
  ☆48Updated 6 years ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years ago
• francois-a / fastqtl
  Enhanced version of the FastQTL QTL mapper
  ☆62Updated last year
• dozmorovlab / excluderanges
  Genomic coordinates of problematic genomic regions as GRanges
  ☆35Updated 2 months ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆84Updated 6 years ago
• billzt / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆48Updated 4 years ago
• ucdavis-bioinformatics-training / 2017_2018-single-cell-RNA-sequencing-Workshop-UCD_UCB_UCSF
  2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF
  ☆35Updated 6 years ago
• jianhong / trackViewer
  A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot
  ☆69Updated last month
• weng-lab / ENCODE-cCREs
  Pipelines to create and analyze ENCODE candidate cis-Regulatory Elements
  ☆20Updated last month
• AndreasHeger / gat
  Genomic Association Tester
  ☆30Updated last year