Alternatives and similar repositories for neoepiscope

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

• vanallenlab / retained-intron-neoantigen-pipeline
  Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.
  ☆28Updated 4 years ago
• jsh58 / DMRfinder
  Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data
  ☆28Updated last year
• cfce / chilin
  ChIP-seq DC and QC Pipeline
  ☆34Updated 4 years ago
• PGDX / cerebro-paper
  ☆23Updated 6 years ago
• ExpressionAnalysis / HLAProfiler
  Using k-mers to call HLA alleles in RNA sequencing data
  ☆22Updated 6 years ago
• ChrisMaherLab / INTEGRATE-Neo
  ☆19Updated 7 years ago
• biosinodx / SCcaller
  Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data
  ☆34Updated 6 months ago
• mandricigor / imrep
  ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.
  ☆28Updated 5 years ago
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆29Updated 2 months ago
• cancerit / alleleCount
  Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…
  ☆45Updated 2 years ago
• gagneurlab / absplice
  ☆39Updated 8 months ago
• shendurelab / MPRAflow
  A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data
  ☆32Updated 4 months ago
• jiujiezz / tsnad
  Detecting somatic mutations and predicting tumor-specific neo-antigens
  ☆28Updated 3 years ago
• tianshilu / QBRC-Neoantigen-Pipeline
  QBRC Neoantigen calling pipeline with CSiN calculation embedded
  ☆24Updated 3 years ago
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated last year
• namphuon / ViFi
  Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
  ☆28Updated 3 years ago
• macarthur-lab / tx_annotation
  Code associated with 2019 manuscript entitled "Transcript expression-aware annotation improves rare variant discovery and interpretation…
  ☆33Updated 3 years ago
• morrislab / pairtree
  Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…
  ☆37Updated last year
• Oshlack / MINTIE
  Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.
  ☆35Updated 11 months ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆31Updated last year
• jfjlaros / demultiplex
  Versatile FASTA/FASTQ demultiplexer.
  ☆33Updated last year
• pachterlab / kma
  Keep Me Around: Intron Retention Detection
  ☆29Updated 6 years ago
• djhn75 / RNAEditor
  ☆15Updated 2 years ago
• mehdiborji / nanoranger
  simplified cellranger for long-read data
  ☆19Updated last month
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• FJD-CEPH / aCNViewer
  Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
  ☆29Updated 6 years ago
• kundajelab / idr
  IDR
  ☆31Updated 2 years ago
• gxiaolab / mountainClimber
  ☆20Updated 5 years ago
• khuranalab / CompositeDriver
  Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
  ☆15Updated 6 years ago
• openvax / isovar
  Assembly of RNA reads to determine the effect of a cancer mutation on protein sequence
  ☆25Updated 7 months ago