ARCHS4 Downloads
This section contains all files created for the ARCHS4 website. The methods are described at
. For help in accessing the files refer to the Help section or contact us directly. The database will be updated on a regular basis and old versions of the files will be accessible.
Expression (gene level)
Human
Mouse
Expression files for mouse and human in HDF5 format. All gene counts are on gene level (Entrez Gene Symbol). For compression purposes the Kallisto pseudocounts are rounded to integer values.
Expression (transcript level)
Human
Mouse
Expression files for mouse and human in HDF5 format. All measurements are at the transcript level (Ensembl ID). For compression purposes the Kallisto pseudocounts are rounded to integer values.
TPM (transcript level)
Human
Mouse
Expression files for mouse and human in HDF5 format. All measurements are at the transcript level (Ensembl ID). The files are very large and values are not rounded.
Expression (GCTx)
Human
Mouse
Expression files for human in GCTx format (BROAD). All measurements are at the gene level level (Entrez Gene Symbol). For more information about the format and software packages refer to this bioRxiv paper.
t-SNE sample coordinates
Human
Mouse
Gene expression reduced to 3 dimensions. The files contain 4 columns with the first 3 containing dimensions x, y, z and the last column containing the numeric part of the GSM id (GSM123456 -> 123456).
t-SNE gene coordinates
Human
Mouse
Gene expression reduced to 3 dimensions. The files contain 4 columns with the first 3 containing dimensions x, y, z and the last column containing Entrez gene symbol.
Gene correlation
Human
Mouse
Pairwise pearson correlation of genes across expression samples.
Pairwise pearson correlation of genes across expression samples. File format is feather and can be loaded directly into memory in Python and R.
JL transfomed expression
Human
Mouse
Gene expression compressed with the Johnson-Lindenstrauss transformation. The RDA files can be loaded into a running R environment with the "load" command. The files create two variables, the transform matrix used for the projection and the jl_expression matrix. The original dimensions are reduced to 1000. The original distances and correlations of the samples should be preserved.
Kallisto index files
Human
Mouse
Kallisto index files used for the alignment process. The index files where build using the Ensembl annotation version 90 and reference cDNA Homo_sapiens.GRCh38.cdna.all.fa.gz and Mus_musculus.GRCm38.cdna.all.fa.gz.
recount2 expression
GTEx
TCGA
Gene counts from GTEx and TCGA from the recount2 project. The reads for these samples was aligned with a different pipeline resulting in significant differences to the ARCHS4 gene expression. Genes that did not overlap with the genes in the ARCHS4 data were removed.
GitHub repository
The scripts used to process the ARCHS4 data are located at the link below. The project is not easily adapted at the current state. We are working on making the software more accessible in the future.
https://github.com/MaayanLab/archs4
