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debarcer
Debarcer: A package for De-Barcoding and Error Correction of sequencing data containing molecular barcodesrobust-paper
Ten Simple Rules for Making Research Software More Robust. Manuscript is published at PLoS Computational Biology. Feedback is welcome!djerba
Create cancer bioinformatics reports from metadata and workflow outputshesmu
Decision-driven action launching systemsequenza
Workflow for Sequenza, cellularity and ploidydashi
Python Dash visualization of OICR QC datavariantEffectPredictor
Variant Effect Predictor WorkflowcfMedipsQc
cfMedipsQC workflow produces a set of metrics files for sequencing data generated in methylation profiling of circulating Free DNA.medips-tools
Scripts for cfMeDIP QC analysishmmcopy
Calls Copy Number Variants on sequencing data from cancer patientswf_cfmedip
Workflow for cfMeDIP data analysis using DockeremSeqQc
Runs bwa-meth followed by bamqc and methyldackelarriba
Fusion caller which runs off of STAR bammalta
Interface and tracking for clinical report generationxenoclassify
A tool for classifiying short-read sequencing data from xenograft samples.modelTsne
A t-SNE framework to visualize OMICs datastrelkaSomatic
Strelka2 somatic variant calling workflowhrDetect
Workflow for the sigtools and HRdetect R packagesdimsum
QC Tracking dashboardercc
workflow for analysis of samples with RNA spike-ins (ERCC)barcodex-rs
Reimplementation of barcodex for performancehlaminer
wrapper workflow for BCGSC tool HLAminersexcmdWorkflow
wdl wrapper for SEXCMD tool. Identification of donor's sex using fastq inputsvidarr
Analysis provenance tracking serverpinery
A LIMS abstraction layer to provide generalized LIMS access via a web service.delly
Delly workflow produces a set of vcf files with different types of structural variant callsmiso-lims-docker
Docker container for miso-limsgsi-ontologies
mutect2
Workflow to run Mutect2 (GATK4)illumina-report
umiConsensus
Workflow to generate consensus sequence bases on UMIs using consensusCruncher.guanyin
Reporting repository and report record keepinghaplotypeCaller
Haplotype caller WDL workflow for GATK4gsi-wdl-tools
rnaSeqQC
RNASeqQC workflowcrosscheckFingerprintsCollector
workflow to generate per library fingerprints for use in gatk CrosscheckFingerprintsqueue_use
Calculate the usage and other stats for an SGE queueestimate
ESTIMATE provides researchers with scores for tumor purity, the level of stromal cells present, and the infiltration level of immune cells in tumor tissues based on expression datagridss
OICR WDL implementation of GRIDSS PURPLE LINXpurple
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