Alternatives and similar repositories for CICERO:

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

• 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…
  ☆43Updated 2 years ago
• Oshlack / Clinker
  Gene Fusion Visualiser
  ☆51Updated 2 years ago
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 6 years ago
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆28Updated 2 weeks ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆45Updated this week
• TrinityCTAT / ctat-mutations
  Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
  ☆74Updated 7 months ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 2 weeks ago
• PGDX / cerebro-paper
  ☆23Updated 6 years ago
• pinellolab / AmpUMI
  Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
  ☆41Updated 9 months ago
• naumanjaved / fingerprint_maps
  Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of func…
  ☆27Updated last year
• zavolanlab / zarp
  The Zavolab Automated RNA-seq Pipeline
  ☆35Updated 2 months ago
• LosicLab / starchip
  Detection of Circular RNA and Fusions from RNA-Seq
  ☆32Updated 6 years ago
• nloyfer / UXM_deconv
  ☆40Updated 2 years ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 6 years ago
• BD2KGenomics / toil-rnaseq
  UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline
  ☆40Updated 4 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆70Updated 4 years ago
• bgruening / galaxy-rna-workbench
  Galaxy RNA workbench
  ☆39Updated 4 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• sfu-compbio / sinvict
  SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
  ☆27Updated 4 years ago
• jason-weirather / hla-polysolver
  Fork of the Polysolver project
  ☆30Updated 5 years ago
• SyntekabioTools / HLAscan
  ☆24Updated 5 years ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆57Updated 4 months ago
• Clinical-Genomics / fusion-report
  Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.githu…
  ☆26Updated 3 months ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 2 years ago
• gagneurlab / absplice
  ☆34Updated 5 months ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• stephenfloor / extract-transcript-regions
  For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…
  ☆35Updated last year
• TRON-Bioinformatics / EasyFuse
  EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
  ☆57Updated 2 months ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆49Updated 7 months ago
• broadinstitute / RNA_MUTECT_1.0-1
  ☆37Updated 5 years ago