| Biological Samples |
| Canine Glioma Patient Samples |
This paper |
Detailed under Table S1
|
| Critical Commercial Assays |
| AllPrep DNA/RNA Mini Kit |
Qiagen |
N/A |
| AllPrep DNA/RNA FFPE Kit |
Qiagen |
N/A |
| KAPA Hyper Prep Kit (Illumina) |
KAPA Biosystems/Roche |
N/A |
| SeqCap EZ Canine Exome Custom Design |
Roche Nimblegen |
canine 140702_canFam3_exomeplus_BB_EZ_HX1 probe set |
| Nimblegen SepCap EZ Kit |
Roche Nimblegen |
N/A |
| KAPA Stranded mRNA-Seq kit |
KAPA Biosystems/Roche |
N/A |
| Premium RRBS Kit |
Diagenode |
N/A |
| Deposited Data |
| DNA sequencing data - WGS and Exome |
This paper |
NCBI SRA Accession ID: PRJNA579792 |
| RNA sequencing data |
This paper |
NCBI SRA Accession ID: PRJNA579792 |
| RRBS sequencing data |
This paper |
NCBI SRA Accession ID: PRJNA579792 |
| Software and Algorithms |
| bwa |
v0.7.15-r1140 |
http://bio-bwa.sourceforge.net/ |
| Genome Analysis ToolKit (GATK) |
v4.0.8.1 |
https://software.broadinstitute.org/gatk/ |
| Qualimap |
v2.2.1 |
http://qualimap.bioinfo.cipf.es/ |
| fastp |
v0.19.5 |
https://github.com/OpenGene/fastp |
| kallisto |
v0.45.0 |
https://pachterlab.github.io/kallisto |
| sleuth |
v0.30.0 |
https://pachterlab.github.io/sleuth |
| FastQC |
v0.11.7 |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc |
| TrimGalore |
v0.5.0 |
https://github.com/FelixKrueger/TrimGalore |
| Bismark Bisulfite Mapper |
v0.19.1 |
https://github.com/FelixKrueger/Bismark |
| Bowtie2 |
v2.2.3 |
N/A |
| NGSCheckMate |
v1.0.0 |
https://github.com/parklab/NGSCheckMate |
| Mutect2 - GATK4 |
v4.0.8.1 |
https://software.broadinstitute.org/gatk/ |
| VarScan2 |
v2.4.2 |
https://github.com/dkoboldt/varscan |
| LoFreq |
v2.1.3.1 |
https://github.com/CSB5/lofreq |
| SomaticSeq |
v3.1.0 |
https://github.com/bioinform/somaticseq |
| Variant Effect Predictor (VEP) |
v91 |
https://github.com/Ensembl/ensembl-vep |
| dNdScv |
0.0.1.0 |
https://github.com/im3sanger/dndscv |
| MuSiC2 |
v0.2 |
https://github.com/ding-lab/MuSiC2 |
| GISTIC2 |
v2.0.22 |
ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTICDocumentation_standalone.htm |
| HMMCopy |
v1.22.0 |
http://bioconductor.org/packages/release/bioc/html/HMMcopy.html |
| TitanCNA |
v1.19.1 |
https://github.com/gavinha/TitanCNA |
| Snakemake |
v5.2.1 |
https://snakemake.readthedocs.io/en/stable/ |
| flowr |
v0.9.10 |
https://github.com/sahilseth/flowr |
| NMF R package |
v0.21.0 |
https://cran.r-project.org/web/packages/NMF |
| Entropy R package |
v1.2.1 |
https://cran.r-project.org/web/packages/entropy |
| outliers R package |
v0.14 |
https://cran.r-project.org/web/packages/outliers/ |
| MutationalPattern R package |
v1.6.2 |
https://bioconductor.org/packages/release/bioc/html/MutationalPatterns.html |
| Palimpsest R package |
v1.0.0 |
https://github.com/FunGeST/Palimpsest |
| BradleyTerryScalable R package |
0.1.0.9000 |
https://cran.r-project.org/web/packages/BradleyTerryScalable/vignettes/BradleyTerryScalable.html |
| DNANexus app for St Jude Cloud data analysis |
v1.1.6 (This paper) |
https://dxapp.verhaaklab.com/dnanexus_ngsapp |
| CIBERSORT |
webserver |
https://cibersort.stanford.edu |
