Tag: Stackify

Pytorch Multi-GPU Issue – Stackify

It is most likely correct. PyTorch only sees two GPUs (therefore indexed 0 and 1) which are actually your GPU 5 and 6. Check the actual usage with nvidia-smi. If it is still inconsistent, you might need to set an environment variable: export CUDA_DEVICE_ORDER=PCI_BUS_ID (See Inconsistency of IDs between ‘nvidia-smi…

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R connection to sqlite – Stackify

SQLite is a file level database, hence to reference it requires a full directory path. No where do you specify the working directory or a full path in the file name. By default, R will use the current working directory contained in getwd(). If database is not contained in this…

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Installation issues with PyMC3 – Stackify

Just had this problem and found a solution. When searching (with Bing or Google) for conda install of pymc3, several links come up. The first is with conda-forge: conda install -c conda-forge pymc3 DO NOT USE THIS or you will get the error messages in the above posts. I have…

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Expressionset – phenodata – Stackify

The correct place for this question is on the Bioconductor support site. It’s better to provide a reproducible example that captures the essence of the problem; creating the reproducible example often helps to identify the reason for the problem. library(Biobase) exprs <- matrix(0, nrow=5, ncol=3, dimnames=list(letters[1:5], LETTERS[1:3])) pData <- data.frame(id=c(“foo”,…

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assign in pandas pipeline – Stackify

You can use pipe: tmp_df = df. drop(“Gene type”, axis=1). rename(columns = { “Gene stable ID”: “ENSG”, “Gene name”: “gene_name”, “miRBase accession”: “MI”, “miRBase ID”: “mirna_name” }). pipe(lambda x: x.assign(species = x.mirna_name.str[:3])) tmp_df Out[365]: ENSG gene_name MI mirna_name species 0 ENSG00000274494 MIR6832 MI0022677 hsa-mir-6832 hsa 1 ENSG00000283386 MIR4659B MI0017291 hsa-mir-4659b…

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