Critical Commercial Assays
|
1.5 Tesla Siemens Sonata and Avanto scanners, 3 Tesla Siemens Trio and Trio TIM scanners |
Siemens Medical Systems, Erlangen, Germany |
N/A |
3 Tesla GE MR750 scanner |
General Electric, USA |
N/A |
Affymetrix 6.0 genotyping array |
Affymetrix, USA |
N/A |
PsychChip genotyping array |
Psychiatric Genomics Consortium, USA |
RRID:SCR_004495 |
OmniExpress genotyping array |
Illumina, USA |
N/A |
Omni 2.5 genotyping array |
Illumina, USA |
N/A |
|
Deposited Data
|
Introgressed Neandertal SNPs |
[18, 20] |
N/A |
GTEx eQTL data |
gtexportal.org |
RRID:SCR_013042 |
BrainSpan Atlas |
http://www.brainspan.org/static/download.html |
RRID:SCR_008083 |
|
Software and Algorithms
|
Globularity measurement script (Mathematica) |
This Study |
N/A |
FreeSurfer (v5.3) |
http://surfer.nmr.mgh.harvard.edu/ |
RRID:SCR_001847 |
FSL FIRST (v5.0, v5.0.9), FLIRT (v6.0) |
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ |
RRID:SCR_002823 |
Avizo |
Thermo Scientific |
RRID:SCR_014431 |
Mathematica |
Wolfram |
RRID:SCR_014448 |
SPM12 |
Wellcome Trust Centre for Neuroimaging, University College London |
RRID:SCR_007037 |
CAT12 toolbox |
Christian Gaser, University of Jena, Germany, http://www.neuro.uni-jena.de
|
N/A |
xjview toolbox |
http://www.alivelearn.net/xjview |
RRID:SCR_008642 |
PLINK |
https://www.cog-genomics.org/plink2/ |
RRID:SCR_001757 |
minimac (release 2012–05-29) |
https://genome.sph.umich.edu/wiki/Minimac |
RRID:SCR_009292 |
mach2qtl |
https://www.unc.edu/~yunmli/software.html |
RRID:SCR_009621 |
IMPUTE (v2.2.2) |
http://mathgen.stats.ox.ac.uk/impute/impute.html |
RRID:SCR_009245 |
QUICKTEST (v0.99b) |
https://wp.unil.ch/sgg/quicktest/ |
N/A |
easyQC |
https://www.uni-regensburg.de/medizin/epidemiologie-praeventivmedizin/genetische-epidemiologie/software/ |
N/A |
METAL |
https://genome.sph.umich.edu/wiki/METAL_Documentation |
RRID:SCR_002013 |
Genomic Type 1 Error Calculator |
http://grass.cgs.hku.hk/gec/ |
N/A |
DESeq2 |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
RRID:SCR_015687 |