Alternatives and similar repositories for SCALPEL

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

• complextissue / pytximport
  Feature-rich Python implementation of the tximport package for gene count estimation.
  ☆41Updated last month
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆62Updated 6 months ago
• gaolabtools / scNanoGPS
  Single cell Nanopore sequencing data for Genotype and Phenotype
  ☆56Updated 7 months ago
• bedapub / splicekit
  splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq
  ☆19Updated 3 weeks ago
• Danko-Lab / proseq2.0
  Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing
  ☆29Updated last year
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆76Updated last year
• LuyiTian / FLAMES
  Full-length transcriptome splicing and mutation analysis
  ☆85Updated last year
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆64Updated 7 months ago
• Xinglab / rMATS-long
  ☆34Updated last month
• StatBiomed / CamoTSS
  Detection and couting alternative TSS in single cells
  ☆16Updated last year
• Dowell-Lab / TFEA
  Transcription Factor Enrichment Analysis
  ☆36Updated last week
• Xinglab / espresso
  ☆64Updated 3 months ago
• XueyiDong / LongReadBenchmark
  Benchmarking long-read RNA-seq analysis tools
  ☆27Updated 10 months ago
• mortazavilab / lapa
  Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.
  ☆31Updated 2 years ago
• WGLab / SCOTCH
  Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single…
  ☆17Updated last month
• shizhuoxing / scISA-Tools
  single-cell-Isoform-Sequencing-Analysis-Tools: New and powerful tools brings single-cell RNA sequencing to the Isoform level and single m…
  ☆26Updated last year
• nf-core / scnanoseq
  Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
  ☆51Updated last month
• TobiTekath / DTUrtle
  Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data. See documentation at:
  ☆20Updated last year
• huyustats / SCATS
  A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
  ☆22Updated 2 years ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆73Updated last year
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆41Updated 3 years ago
• gatk-workflows / gatk4-rnaseq-germline-snps-indels
  Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
  ☆82Updated 4 years ago
• gexijin / shinygo
  ☆33Updated last month
• Genentech / Isosceles
  The Isoforms from Single-Cell; Long-read Expression Suite
  ☆36Updated 11 months ago
• ay-lab / FitHiChIP
  Statistically Significant loops from HiChIP data
  ☆46Updated last year
• smithlabcode / ribotricer
  A tool for accurately detecting actively translating ORFs from Ribo-seq data
  ☆39Updated 10 months ago
• JinLabBioinfo / DeepLoop
  DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data
  ☆34Updated 8 months ago
• zanglab / SICER2
  ☆23Updated 9 months ago
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆31Updated 9 months ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago