Blog Posts | My bits

Dec 9, 2023 1 min read

3D-printer WALL-E toilet paper holder

Finally tired of the broken TP holder and how to make a trip to Home Depot a 2 months project.

Last updated on Sep 30, 2023 6 min read

My story with cancer - Jimmy fund walk Oct 1st

My personal experience with cancer and how much work still to do

Oct 3, 2019 5 min read

My transition to biotech

My personal experience giving up on academia to bet on industry

Jul 19, 2019 1 min read

kallisto-bustools

       JobID                        JobName      NCPUS     MaxRSS     AveRSS  Elapsed
------------ ------------------------------ ---------- ---------- ---------- ----------

14150319                             index          2     91.06G          0   01:26:32

14153823                          kallisto          2     67.28G     65.34G   00:59:35

14156768                       bus-correct          4      1.19G      1.19G   00:01:29

14156812                  bus-capture-cdna          4     16.16G     10.22G   00:07:59

14156835                bus-capture-intron          4     16.27G     16.27G   00:06:54

Jul 11, 2019 5 min read

How to set up cellranger to make your hpc admin happy

I found myself to force to use cellranger. Meanwhile it helps a lot to run from bcl files to single cell counts matrixes, I discovered that is quite difficult to control many options related to optimization.

Apr 5, 2019 2 min read

How to set up public dataset analysis with bcbio-nextgen

We use bcbio-nextgen for the analysis of sequencing data, mainly, (sc)RNAseq, smallRNAseq, DNASeq and ChIPSeq. It is not rare that we get collaborators who wants to re-analyze public data-set.

Inside bcbio, we have bcbio_prepare_samples.py to help to merge multiple files that belong to the same sample into one file to make easier the configuration of bcbio. We extended this script to pull down data from GEO and SRA repository.

Sep 21, 2018 5 min read

Get colors for your heatmap annotation

This post will show how to configure quickly the colors for the annotation of rows/columns that go on top or on the side of a heatmap.

I normally use pheatmap a lot. Recently I discovered ComplexHeatmap. In both cases I spend always sometime changing the colors of the annotations. I ended up coding a function inside my package DEGreport to do that.

Aug 12, 2018 4 min read

How to plot miRNA, gene expression and functional analysis together

This post should show you an easy way to get the following data type integrated into a figure:

functional enrichment analysis
gene expression data from any technology
miRNA expression data from any technology

I am using the function isoNetwork from the package isomiRs, that of course is developed by me :) My ego is not that big, it is just I wanted a figure showing that information, and I couldn’t find any at a time, but if you know any, tweet me about it to @lopantano.

Aug 23, 2017 4 min read

Subset of object creates bigger RDA file size than original object

This is a funny story, and I will try to tell you how I realized I don’t know anything about R in 400 words.

I work at the Bioinformatic Core at Harvard TH School. People who know us, or collaborate with us, knows that we mainly use bcbio to analyze sequencing data (check it out, super cool tool).

Mar 20, 2017 2 min read

DEGreport to plot nice RNA-seq figures

Differentially gene expression analysis with RNA-seq data is quite common nowadays, and there are pretty good Bioconductor packages for that: limma::voom, DESeq2 …

The code for that part is quite simple, being super quick to get a list of de-regulated genes. However, downstream analyses vary a lot depending on the project itself. But I found myself doing the same plots and analyses many times for different project, so I put together a bunch of plots and analyses using code from my colleagues at work (@HSPH bioinformatics core) and myself.