Directly reprogrammed myoblasts

  • 22 Jul 2020

    Getting gene attributes from biomart

    Biomart is an Ensembl service for querying and retrieving data. Here I’ll use R/Bioconductor to get gene positions for a list of genes. We basically need a mart object which encapsulates ...

  • 21 Jul 2020

    Bioconductor and Docker

    Dockerizing your bioconductor code is one way to ensure a reproducible workflow. It also enables easier deployment to cloud environments (e.g. AWS Batch) in case you want to scale your analysis. ...

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  • Getting gene attributes from biomart

    Biomart is an Ensembl service for querying and retrieving data. Here I’ll use R/Bioconductor to get gene positions for a list of genes. We basically need a mart object which encapsulates the species, host and database information. Here I’m using the US west coast mirror. This defaults to the current build (GRCh38) of the human...

  • Bioconductor and Docker

    Dockerizing your bioconductor code is one way to ensure a reproducible workflow. It also enables easier deployment to cloud environments (e.g. AWS Batch) in case you want to scale your analysis. The official Bioconductor docker containers are hosted on Docker Hub. They are built with Rstudio-server installed so that you can run an interactive analysis....

  • Working with Pacbio IsoSeq data

    Overview With its long single molecule reads, Pacbio IsoSeq offers the tantalizing possibility of reading entire full-length RNAs. The library prep is not for the faint of heart and a recent provider asked me for 5ug of RNA to start – not an easy task! Moreover, a thorough interrogation of a transcriptome would require at...

  • Favorite atom packages

    hydrogen atom-beautify autocomplete-python busy-signal goto-definition highlight-selected linter-flake8 markdown-writer minimap python-autopep8 symbols-tree-view script ftp-remote-edit

  • Assembling reads with velvet

    Velvet is a hash-based deBrujin assembler. I occasionally use it to build contigs from short read RNAseq data, although it can be used for long reads, metagenomics, etc. To install, just download, extract and make. There are two parts to the program: 1. velveth – prepare the sequences 2. velvetg – build the graph and...