Tools List
Public Tools
Annotation Apps
Data Transfer Apps
DNAseq Apps
gatk4_bqsr_parallel
Variant calling
gatk4_haplotypecaller_parallel
Variant calling, post-alignment QC
gatk4_genotypegvcfs_single_sample_parallel
Variant calling
picard_mark_duplicates
Variant Calling- remove duplicates, post-alignment
GWAS Apps
File Transfer Apps
Import Apps
Interactive Analysis Apps
cloud_workstation
N/A
SSH-accessible unix shell on a platform cloud worker. Use it for on-demand analysis of platform data.
ttyd
N/A
Unix shell on a platform cloud worker in your browser. Use it for on-demand CLI operations and to launch https apps on 2 extra ports
Joint Genotyping Apps
Mapping Manipulation Apps
PheWAS Apps
PRS Apps
QC Apps
Quantification Apps
salmon_mapping_quant
Salmon
Transcriptomics Expression Quantification
Read Mapping Apps
bowtie2_fasta_indexer
bowtie2
: bowtie2-build
Building reference for Bowite2 alignment
bowtie2_fastq_read_mapper
bowtie2
, SAMtools view, SAMtools sort, SAMtools index
Short read alignment
star_generate_genome_index
STAR (Spliced Transcripts Alignment to a Reference) (--runMode genomeGenerate)
RNA Seq- indexing
salmon_mapping_quant
Salmon
Transcriptomics Expression Quantification
Read Manipulation Apps
gatk4_bqsr_parallel
Variant calling
RNAseq Apps
star_generate_genome_index
STAR (Spliced Transcripts Alignment to a Reference) (--runMode genomeGenerate)
RNA Seq- indexing
star_generate_genome_index
STAR (Spliced Transcripts Alignment to a Reference) (--runMode genomeGenerate)
Transcriptomics Expression Quantification
star_mapping
STAR (Spliced Transcripts Alignment to a Reference)
Transcriptomics Expression Quantification
salmon_mapping_quant
Salmon
Transcriptomics Expression Quantification
RNAseq Notebooks
Transcript_Expression_Part-02_Analysis-diff-exp_R.ipynb
DESeq2
Transcript_Expression_Part-03_Analysis-GSEA_R.ipynb
WebGestaltR
Transcript_Expression_Part-04_Analysis-CoEx-Network_R.ipynb
WGCNA, topGO
Transcript_Expression_Part-05_Analysis-Regulatory-Network_R.ipynb
GENIE3
Utility Apps
swiss-army-knife
bcftools
, bedtools
, bgzip
, plink
, sambamba
, SAMtools
, seqtk
, tabix
, vcflib
, Plato
, QCTool
, vcftools
, plink2
, Picard
, REGENIE
, BOLT-LMM
, BGEN
Data processing tools
ttyd
N/A
Unix shell on a platform cloud worker in your browser. Use it for on-demand CLI operations and to launch https apps on 2 extra ports
Variant Calling Apps
gatk4_haplotypecaller_parallel
Variant calling, post-alignment QC
gatk4_genotypegvcfs_single_sample_parallel
Variant calling
picard_mark_duplicates
Variant Calling- remove duplicates, post-alignment
gatk4_mutect2_variant_caller_and_filter
Somatic variant calling and post calling filtering
gatk4_somatic_panel_of_normals_builder
Create a panel of normals (PoN) containing germline and artifactual sites for use with Mutect2.
Visualization Apps
Titan Tools
Statistics Apps
dxjupyterlab
dxpy
, matplotlib
, numpy
, pandas
, papermill
, scipy
, seaborn
, dxdata
, cntk
, keras
, scikit-learn
, TensorFlow
, torch
Running analyses, visualizing data, building and testing models and algorithms in an interactive way
dxjupyterlab
dxpy
, matplotlib
, numpy
, pandas
, papermill
, scipy
, seaborn
, dxdata
, BiocManager
, coloc
, epiR
, hyprcoloc
, incidence
, MendelianRandomization
, outbreaks
, prevalence
Running analyses, visualizing data, building and testing models and algorithms in an interactive way
dxjupyterlab
dxpy
, matplotlib
, numpy
, pandas
, papermill
, scipy
, seaborn
, dxdata
, BiocManager
, coloc
, epiR
, hyprcoloc
, incidence
, MendelianRandomization
, outbreaks
, prevalence
, Stata
, stata_kernel
Running analyses, visualizing data, building and testing models and algorithms in an interactive way, accessing and manipulating data in spark databases and tables
dxjupyterlab
dxpy
, matplotlib
, numpy
, pandas
, papermill
, scipy
, seaborn
, dxdata
, nipype
, freesurfer
, FSL
Running imaging processing related analysis
Apollo Tools
Dataset Administration Apps
Dataset Management Apps
Data Science Apps
dxjupyterlab_spark_cluster
dxpy
, hail
, matplotlib
, numpy
, pandas
, papermill
, scipy
, seaborn
, dxdata
, pyOpenSSL
, glow.py
, pypandoc
, koalas
, pyarrow
, bokeh
, vep
, BiocManager
, coloc
, epiR
, yprcoloc
, incidence
, MendelianRandomization
, outbreaks
, prevalence
, sparklyr
, Glow
Running analyses, visualizing data, building and testing models and algorithms in an interactive way
dxjupyterlab_spark_cluster
dxpy
, hail
, matplotlib
, numpy
, pandas
, papermill
, scipy
, seaborn
, dxdata
, pyOpenSSL
, glow.py
, pypandoc
, koalas
, pyarrow
, bokeh
, vep
, BiocManager
, coloc
, epiR
, yprcoloc
, incidence
, MendelianRandomization
, outbreaks
, prevalence
, sparklyr
, HAIL
Running analyses, visualizing data, building and testing models and algorithms in an interactive way
dxjupyterlab_spark_cluster
dxpy
, hail
, matplotlib
, numpy
, pandas
, papermill
, scipy
, seaborn
, dxdata
, pyOpenSSL
, glow.py
, pypandoc
, koalas
, pyarrow
, bokeh
, vep
, BiocManager
, coloc
, epiR
, yprcoloc
, incidence
, MendelianRandomization
, outbreaks
, prevalence
, sparklyr
, HAIL
, Ensembl Variant Effect Predictor
Running analyses, visualizing data, building and testing models and algorithms in an interactive way
Third Party Tools
Tools in this section are created and maintained by their respective vendors and may require separate licenses.
DNAseq Apps
sentieon-tnseq
Sentieon's FASTQ to VCF somatic analysis pipeline
WGS, WES, accelerated analysis
sentieon-bwa
Sentieon's FASTQ to BAM/CRAM pipeline
WGS, WES, accelerated analysis
pbgermline
BWA-Mem Alignment, Co-ordinate Sorting, Picard MarkDuplicates, Base Quality Score Recalibration
WGS, WES, accelerated analysis
sentieon-tnbam
Sentieon's BAM to VCF somatic analysis pipeline
WGS, WES, accelerated analysis
pbdeepvariant
Deepvariant
Variant calling, accelerated analysis
sentieon-umi
Sentieon's pre-processing and alignment pipeline for next-generation sequence
WGS, WES, accelerated analysis
sentieon-dnabam
Sentieon's BAM to VCF germline analysis pipeline
WGS, WES, accelerated analysis
sentieon-joint_genotyping
Sentieon GVCFtyper
WGS, WES, accelerated analysis
sentieon-ccdg
Sentieon's FASTQ to CRAM pipeline, Functional Equivalent Pipeline
WGS, WES, accelerated analysis
sentieon-dnaseq
Sentieon's FASTQ to VCF germline analysis pipeline
WGS, WES, accelerated analysis
Joint Cohort Genotyping Apps
sentieon-joint_genotyping
Sentieon GVCFtyper
WGS, WES, accelerated analysis
Read Mapping Apps
sentieon-tnseq
Sentieon's FASTQ to VCF somatic analysis pipeline
WGS, WES, accelerated analysis
sentieon-bwa
Sentieon's FASTQ to BAM/CRAM pipeline
WGS, WES, accelerated analysis
pbgermline
BWA-Mem Alignment, Co-ordinate Sorting, Picard MarkDuplicates, Base Quality Score Recalibration
WGS, WES, accelerated analysis
pbdeepvariant
Deepvariant
Variant calling, accelerated analysis
sentieon-umi
Sentieon's pre-processing and alignment pipeline for next-generation sequence
WGS, WES, accelerated analysis
sentieon-ccdg
Sentieon's FASTQ to CRAM pipeline, Functional Equivalent Pipeline
WGS, WES, accelerated analysis
sentieon-dnaseq
Sentieon's FASTQ to VCF germline analysis pipeline
WGS, WES, accelerated analysis
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