.spelling

# markdown-spellcheck spelling configuration file
# Format - lines beginning # are comments
# global dictionary is at the start, file overrides afterwards
# one word per line, to define a file override use ' - filename'
# where filename is relative to this configuration file
# Companies
Aspera
Auth0
BeautifyTools
Dana-Farber
DNAnexus
DocuSign
Gmail
OpenSeaDragon
OpenSSH
macOS
Plotly
PowerShell
PubMed
SJCRH
SQLite
termdb
# Packages/Languages/Tools
bioconda
conda
D3
D3.js
JavaScript
jQuery
linux
miniconda
Node.js
proteinpaint
proteinpaint's
pypi
python3
quay.io
sjcharts
ubuntu
# URLs
dnanexus.com
http
https
pecan.stjude.org
pecan.stjude.org.
proteinpaint.stjude.org
scmc.com.cn
stjude.org
stjude.cloud
www.biorxiv.org
www.dnanexus.com
www.htslib.org
www.ncbi.nlm.nih.gov
www.stjude.cloud
# Names
Abdulgafoor
Alexandrov
Aman
Anders
Ashiqul
Babraham
Bangur
Beisi
Benjamini-Hochberg
Benshang
Bensheng
Bergstrom
Cheng
Chunliang
Daly
Delaram
Dongren
E.N.
Easton
Edmonson
Finkelstein
Foy
Frantz
Geralyn
Haradhvala
Hu
Hyle
Irina
J.Z.
Jian
Jinghui
Jobin
Ju
Kandali
Klco
Kolekar
L.B.
Liqing
Liu
Ludmil
M.N.
Mahto
Maoxiang
McMurry
Meshinchi
Mudunuri
Mullighan
N.J.
Naina
Nakitandwe
Nedra
Pamella
Pandurang
Pappo
Qian
Rahul
Rahbarinia
Ren
Robison
Rusch
Serang
Shaela
Shaner
Shao
Shaohua
Shaoyan
Shen
Shuhong
Shuoguo
Sioson
Soheil
Suh
Swistak
Szlachta
Thangaraj
Ti-Cheng
Tian
Treadway
Tuan
Vijay
Xiang
Xiaolong
Xiaotu
Xin
Xing
Y.L.
Yanling
Yasui
Ying
Yongjin
Yu
Yutaka
Zhang
Zhaoming
Zhou
# Genomics/Biology Terms
BAM
BamToGFF
BAMs
bioinformatics
biomarker
biomarkers
Bowtie
bsub
chr
chr1
chr2
chr5
chr6
chr7
chr9
chr10
chr11
chr12
chr13
chr16
chr22
chrx
cis-x
ClinGen
ClinVar
cnv
CNVs
CompBio
CompBioID
contig
contigs
Discov
DMG-H3K27a
epigenetic
epigenetics
epigenomic
exome
exonic
exons
fastq
FastQC
FASTQs
FileViewer
fpkm
FPKMlog2
fuzzion
Gemcitabine
GenomePaint
germline
GRCh37
GRCh37-lite
GRCh38
GRCh38_no_alt
gVCF
heatmap
heatmaps
hematopoietic
heterozygosity
H3K27A_EVOLUTION
hg19
hg38
hg39
htseq
htseq-count
htslib
indel
indels
isoform
isoforms
JSON-BED
Kaplan-Meier
liftover
log10
log2
Log2Fold
LogRatio
lymphoblastic
medulloblastoma
methylation
MethylationToActivity
missense
multi-omic
multi-omics
MYCN-ATRX
Myelodysplastic
neuroblastoma
noncoding
nt
omics
oncoprint
OncoTree
osteosarcoma
PanALL
pathogenecity
PAX5-JAK2
Paxalisib
PedAML
plotMDS
ProteinPaint
proteomic
PolyA
pubmed
RefSeq
Ribociclib
rnaseq
SamToFastq
samtools
SEAseq
SequencErr
SigProfiler
SNP
SNPs
snvindel
snv
SNVs
strandedness
sv
svcnv
SVs
T-ALL
T-ALLs
t-SNE
tMN
transcriptomic
transcriptomics
tSNE
tStat
unmap
unstranded
VCFs
vcftools
Voom
WGS
WES
wilms
XenoCP
xenograft
# Azure/Cloud Terms
subnet
subnets
uswest
westus
# Files
BMF_MDS-Schedule1
CCSS-Schedule1
ClinGen-Schedule1
DMG-H3K27a-Schedule1
MBPRG-Schedule1
MBPRP-Schedule1
PanALL-Schedule1
PBTP-Schedule1
PCGP-Schedule1
PedAML-Schedule1
SGP-Schedule1
SJLIFE-Schedule1
RPAML-Schedule1
tMN-Schedule1
# File Extenstions
bai
bam
bam.bai
bb
bgz
bw
csi
gz
gz.tbi
h5
hdf5
html
pdf
tbi
txt
vcf
xlsx
# General/Other Terms
_
_blank
a.k.a.
adhoc
autofill
autogenerate
autosave
autosaved
autoscale
backend
basename
boolean
bgzip
breakpoint
bulleted
CD-20-1230
checkbox
checkboxes
config
configs
customizable
dataset
datasets
deduplication
denormalize
denormalized
dropdown
e.g.
entrypoint
entrypoints
genomically
gif
gzip
gzipped
hardcode
hardcoded
histotypes
hostname
i.e.
ing
interquartile
Jiangsu
Jiao
metadata
MiB
mm9
mm10
natively
navbar
nonsynonymous
parameterized
performant
permalink
popup
precalculate
precalculated
preconfigure
preconfigured
prefill
prefilled
prefilter
preinstalled
prepended
prepopulate
prepopulated
PubMedID
quickstart
readme
reprovisioned
requester
requesters
reupload
reuploaded
rgb
rgba
roadmap
runtime
runtimes
signee
stjudecloud-helpdesk
subcommand
subcommands
substep
substeps
todo
tooltip
translocating
U.S.
unharmonized
unpublish
url
urls
virtualized
walkthrough
whitelist
# Genomics Platform/DNAnexus Specific
counts.txt
DAU
DAUs
dx-toolkit
dx
HiSeq
NovaSeq
dxid
SAMPLE_INFO.txt
# PeCan Specific
athogenicity
cer
dbNSFP
diatric
Entrez
ex-TCGA
ExAC
MutationAssessor
nformation
non-TCGA
PolyPhen2
SigProfilerExtractor
v1.1.20
v3.3
xchange
# Viz Specific
aicheck
amongst
bampile
boxplot
boxplots
convolutional
coverage-vaf
dbSNP
dbSNPs
Ensembl
hotspot
intergenic
intragenic
intron
intronic
NM_000546
NM_000546.5
overlayed
rnaPosition
runproteinpaint
Sampletype
splice-region
splice_region
stopgain
stoploss
strikethrough
strikethroughs
studyview
subsampling
Survivorship
tabix
utr3
utr5
utr_3
utr_5
VisCom
VisEditor
# Prose Components from Nuxt
callout
# Icons
i-heroicons-arrows-right-left
i-heroicons-bug-ant
i-heroicons-document-text-solid
i-heroicons-exclamation-circle
i-heroicons-light-bulb

- content/2.genomics-platform/2.about-our-data/2.file-formats-and-sequencing-information.md
bwa
chrom
haplotype
in-silico
loc.end
loc.start
MutationTaster
Pre-annotation
StrongARM
v100
v2.7.1a
v2.7.1a.
validation_status

- content/2.genomics-platform/2.about-our-data/4.st-jude-cloud-disease-ontology.md
2024.02.09.579680v1.full
astrocytoma
chondroblastic
CIC-rearranged
composable
desmoplastic
Dysembryoplastic
ependymal
Ependymoma
glioblastoma
Glioneuronal
ICD-O
molecularly
Myxopapillary
Neuroepithelial
NKX2-1
non-WNT
ontologies
osteoblastic
pmc
Rhabdoid
SJC-DO
subtyping
Supratentorial
v0
v0.0
v0.1
v0.1.
v0.2
v0.2.
Umeda
pAML
myelodysplasia-related
Myelomonocytic
Megakaryoblastic
WHO5-aligned
GLISr
AMLs

- content/2.genomics-platform/3.managing-data/2.upload-download-data-local.md
3.X

- content/2.genomics-platform/4.analyzing-data/2.running-our-workflows.md
Neoepitope

- content/2.genomics-platform/4.analyzing-data/3.creating-a-cloud-app.md
dx-fastqc-example-app
execDepends
fastqc-report
runSpec
v0.11.8
v0.291.1

- content/2.genomics-platform/4.analyzing-data/4.interactive-nodes.md
mem1_ssd1_x2

- content/2.genomics-platform/4.analyzing-data/5.visualizing-ngs-data.md
v2.0.0

- content/2.genomics-platform/5.workflow-guides/1.chipseq.md
50bp
dm3
H2A.Z
H3K27ac
H3K27me3
H3K36me3
H3K4me1
H3K4me2
H3K4me3
H3K79me2
H3K9-14ac
H3K9me1
H3K9me2
H3K9me3
Illumina-generated
Immunoprecipitation
Sample_R1.fastq.gz
Sample_R2.fastq.gz

- content/2.genomics-platform/5.workflow-guides/2.cisx.md
3.30872245021211e
4.60632106249222e
4.69553625126628e
5S_rRNA
6.10351562500001e
6.11761294450693e
6.66361745922277e
ai_all_markers
ai_ase_markers
Alternative_Allele
alternative_normal_count
alternative_tumor_count
aneuploidy
antisense
ase_markers
ase_outlier
average_ai_all
average_ai_ase
bi_cohort
Bonferroni
candidate.group
cdsEndStat
cdsStartStat
Chr_Allele
chrA
chrB
chrom
cis-activated
cis-activation
cmpl
comb.pval
cvg_rna
cvg_wgs
delta.abs
ENSG00000249352.3
ENSG00000261122.2
Epigenomics
EpiRoadmap_dyadic
EpiRoadmap_enhancer
EpiRoadmap_promoter
fpkm.raw
GeneID
GeneName
gsym
imprinting.status
incmpl
iPSC
kilobase
left.candidate.inTAD
lincRNA
loc.end
loc.start
logR
loo.cohort.size
loo.pval
loo.rank
loo.source
mean.delta
mut_freq_rna
mut_freq_wgs
na
NM_003189
NM_015423
NM_024684
NM_145804
ortA
ortB
p.bi
p.cohort
p.white
posA
posB
pvalue
pval_all_markers
pval_ase_markers
rank.bi
rank.cohort
rank.white
rawp
reference_normal_count
reference_tumor_count
right.candidate.inTAD
ref.1
SampleID
seg.mean
size.bi
size.cohort
size.white
SJALL018373_D1
tf
unk
v10
white_list

- content/2.genomics-platform/5.workflow-guides/3.methylation-to-activity.md
1000bp
bisulfite
chrom
CpG
EnsmblID_G
EnsmblID_T
H3K27ac
H3K4me3
methylomes
mval
mvalue
Predicted_log2_ChipDivInput_
RStart
SampleName_Input.bw
SampleName_H3K27ac.bw
SampleName_H3K4me3.bw

- content/2.genomics-platform/5.workflow-guides/4.mutational-signatures.md
mtsg
SigProfilerMatrixGenerator
SJMEL001001_D1
SJNBL001_D
Subs-01

- content/2.genomics-platform/5.workflow-guides/5.rapid-rnaseq.md
Coverage_bw
ITDs
KIAA1549-BRAF
nontemplated
qc_clean_reads
qc_perfect_reads
readthrough
refGene
RNApeg
Sample.bam
Sample_R1.fastq.gz
Sample_R2.fastq.gz
Trimmomatic

- content/2.genomics-platform/5.workflow-guides/6.rnaseq-expression-classification.md
batch_corrected
covariates
Gencode
Farber
input_counts
library_type
original_matrix
read_length
Rtsne
sample_name
Sample.bam
Sample.counts.txt
tsne_output
variance_stabilized
varianceStabilizingTransformation
v31

- content/2.genomics-platform/5.workflow-guides/7.seaseq.md
100bp
BAM_Density
BAM_files
bedtools
bowtie
CentriMo
FRiP
H3K27Ac
PEAKS_Annotation
PEAKS_Display
SpaMO
SRRs
tdf
v1

- content/2.genomics-platform/5.workflow-guides/8.sequencerr.md
aln
bwa
doi
E.M.
fcut
flowcell
PairError
pairError.txt
s13059-020-02254-2
Sample.bam
Sample.bam.bai

- content/2.genomics-platform/5.workflow-guides/9.warden.md
condition1
condition1.png
condition2
GSEA.input.
GSEA.tStat.
ifferential
Limma
MA_plot.condition2
nalysis
orkflow
Sample1.bam
Sample2.bam
Sample1.fastq.gz
Sample2.fastq.gz
Sample1.htseq
Sample2.htseq
samplesheet.txt
samplesheet.xlsx
Sample_sheet.txt
Sample_sheet.xlsx
v2.5.3a
v24
v31
xpressio

- content/3.pecan/1.overview/2.methods-and-data.md
DESeq2
DESeq2's
NCI-TARGET
de
novo

- content/3.pecan/2.data-facets/1.variants.md
pathogneic
whole-transcriptome

- content/3.pecan/2.data-facets/3.expression.md
4f
MoR

- content/3.pecan/2.data-facets/4.histology.md
Slidescale

- content/3.pecan/3.pecan-pie/1.what-is-pie.md
app-stjude_medal_ceremony
app-stjude_vep_plus
pecanpie_ASHG_2017.pptx

- content/3.pecan/3.pecan-pie/2.faq.md
medaling
pre-HTSlib
table_S1_gene_list_5_categories_v2.xlsx
TCGA-subtracted
vcf-validator
vcftools

- content/4.visualization-community/1.overview/1.what-is-visualization-community.md
1k

- content/4.visualization-community/1.overview/3.data-types-and-graphs.md
FusionEditor
Ase
MAF-timeline

- content/4.visualization-community/2.getting-started/3.how-to-use-the-viseditor.md
mode_hm
pyramidup
refgene
un
unhide

- content/4.visualization-community/2.getting-started/5.manage-your-data.md
24h
ppr1

- content/4.visualization-community/3.code-block-library/1.code-block-basics.md
30m

- content/4.visualization-community/3.code-block-library/3.arc.md
bedfile
bedindexURL
bedURL
mode_arc
mode_hm
percentile_max

- content/4.visualization-community/3.code-block-library/8.hi-c.md
percentile_max
pyramidup

- content/4.visualization-community/3.code-block-library/13.profile-gene-value.md
pvg

- content/4.visualization-community/4.proteinpaint/5.viewing-snv-indel-mutations.md
p.R248Q
heterozygosity

- content/4.visualization-community/4.proteinpaint/6.viewing-gene-fusions.md
1b

- content/4.visualization-community/4.proteinpaint/12.using-the-heatmap.md
1q
5p
borderwidth
cellbg
heatmapJSON
metadatabymatrix
metadatabymatrix.terms
sampleannotation
samplegroup
sampletype
sortorder

- content/4.visualization-community/4.proteinpaint/14.stratifying-mutations-by-cancer-subtype.md
Non-BS-HGG

- content/4.visualization-community/4.proteinpaint/15.snv-and-indel.md
aachange
frameshift
maf-coverage
mutant_in_normal
mutant_in_tumor
proteinDel
proteinIns
refseq
splice_region
sampletype
total_in_normal
total_in_tumor

- content/4.visualization-community/4.proteinpaint/16.sv-and-fusion-transcript.md
chr_a
chr_b
gene_a
gene_b
isoform_a
isoform_b
position_a
position_b
strand_a
strand_b

- content/4.visualization-community/4.proteinpaint/18.internal-tandem-duplications.md
chr_start
chr_stop
rnaDuplength

- content/4.visualization-community/4.proteinpaint/19.intragenic-deletion.md
chr_start
chr_stop
rnaDellength
rnaDuplength

- content/4.visualization-community/4.proteinpaint/20.truncation.md
Losstype

- content/4.visualization-community/4.proteinpaint/21.json-bed.md
cdslen
chromHMM
codingstart
codingstop
itemurl_appendname
mRNA
onerow
rnalen
stackheight
stackspace
translatecoding
UTRs

- content/4.visualization-community/4.proteinpaint/22.splice-junction.md
cohortsetting
sample1
sample2

- content/4.visualization-community/4.proteinpaint/23.profile-gene-value.md
chromHMM
genevaluematchname
genevaluetklst
genevaluetrack
genevaluetype
legendimg
phosphorylation
proteomics
sampleID

- content/4.visualization-community/4.proteinpaint/24.bampile.md
bampilefile
Basepair
SAMPLE.gz
SAMPLE.gz.tbi
v6.0

- content/4.visualization-community/4.proteinpaint/26.using-custom-tracks.md
allheight
bedj
bigwigstranded
bottompad
dotplotfactor
fineheight
fineymax
hide_cnvgain
hide_cnvloss
indexURL
isdense
isfull
mdssvcnv
midpad
ncolor
ncolor2
pcolor
pcolor2
profilegenevalue
sampleAttribute
sampleset
singlesample
strand1
strand2
tabix-indexed
toppad
Typecode
usegrade
VAF-coverage

- content/4.visualization-community/4.proteinpaint/30.loading-tcga-maf-file.md
cDNA_Change
Hugo_Symbol
PR_TCGA_SKCM_PAIR_Capture_All_Pairs_QCPASS.aggregated.capture.tcga.uuid.somatic.maf
Protein_Change
Refseq_mRNA_Id
Start_position
Tumor_Sample_Barcode
Variant_Classification

- content/4.visualization-community/4.proteinpaint/31.using-vcf-file.md
3_prime_UTR_variant
5_prime_UTR_variant
als
altalleleinfo
Amino_acids
autocategory
boxplotvaluekey
c.1799T
chromosome.position.REFallele.ALTallele
coding_sequence_variant
cohort_VCF
col_separator
CSQ-like
downstream_gene_variant
ENST00000288602.6
Entrez
Existing_variation
feature_elongation
feature_truncation
Feature_type
file.vcf
file.vcf.gz
file.vcf.gz.tbi
frameshift
frameshift_variant
HGVSc
HGVSp
incomplete_terminal_codon_variant
indexURL
inframe_deletion
inframe_insertion
info2singletable
info2table
intergenic_variant
intron_variant
Key2color
Key4annotation
locusinfo
lst
makeurl
mature_miRNA_variant
missense_variant
NMD_transcript_variant
non_coding_transcript_exon_variant
non_coding_transcript_variant
numericCutoff
numericCutoffSide
numericfilter
populationfrequencyfilter
protein_altering_variant
proteindel
proteinindel
proteinins
Protein_position
regulatory_region_ablation
regulatory_region_amplification
regulatory_region_variant
sampleannotation
sampleannotation.annotation
sampleannoationkey
samplenamemap
sampletype
serverconfig.json
SnpEff
splice_region
splice_acceptor_variant
splice_donor_variant
splice_region_variant
start_lost
stop_gained
stop_lost
stop_retained_variant
synonymous_variant
TF_binding_site_variant
TFBS_ablation
TFBS_amplification
transcript_ablation
transcript_amplification
upstream_gene_variant
url4variant
vaf2coverageplot
variant2img
variant2img.ext
variant2img.path
Variantsunburst
variant_VCF
vcfcohortrack
vcfinfofilter
vcfurl

- content/4.visualization-community/4.proteinpaint/32.embedding-proteinpaint.md
altallele
dataname
dbexpression
dt
fimo
hiddenclass
hide_cnvgain
hide_cnvloss
hlaachange
isdense
isfull
isgenevalue
isgenevalueonesample
itd
loh
mnv
mutationset
negStrand.bw
posStrand.bw
querykey
refallele
refgene
repeatmasker
sampleAttribute
samplelst
sampleset
sampleselectable
singlesample
SPLICE_REGION
stackheight
upperlengthlimit
yourpage.html
yourvariable
yourvariable.node

- content/4.visualization-community/4.proteinpaint/33.url-parameters.md
v2.0

- content/4.visualization-community/4.proteinpaint/34.study-view.md
assaytracks
bedgraph
Browserview
Config.categories
config.jtype2color
datadir
Dbexpression
dbexpression.attrlst
dbexpression.dbfile
dbexpression.tablename
dbexpression.tidy
dMAF
file2
geneset
hardcodemap.metadata
H3K4me3
level1
level2
metadataTsv
MinN
mutationset
Mutant_allele
nMAF
numeric2
passwd
patientannotation.annotation
patientannotation.metadata
patient-sampletype
readdepthcutoff
Reference_allele
RNApeg
rna_seq
rsNumber
samplekeys
samplename
Sampletype
sankey
sankey.genes
sankey.geneset
svfusion
TinD
TinN
track1
track2
track.gz
trackfacets
Variant_gene_assoc
vafs1
Vcf_cohort

- content/4.visualization-community/5.genomepaint/2.genomepaint-user-guide.md
amplicon
ase
atrx
BAF-0
bcftools
chrA
chrB
dna_assay
DNS-compliant
dt
ETV6-ABL1
FILE.sorted.gz
FILE.sorted.gz.tbi
FILE.sorted.vcf.gz
FILE.sorted.vcf.gz.tbi
fpkm_URL
in-situ
log2ratio
mattr
overexpression
Pediatric2
posA
posB
pre-annotate
segmean
seg.mean
SH-SY5Y
subsetting
svcnv
tabix
TCGA_DLBC
strandA
strandB
survdiff
svcnvfpkmurl
svcnv_URL
vcf_URL