About this page

04.38 pm 20.11.2024 IST

For those new here, I'm a scientist. An RNA biologist by training. A bench scientist who loves tinkering with biology as much as tinkering with computers. Playing with code and exploring new pipelines is one of my favourite things to do when the wet work moves slow. It's an unusual hobby for a biologist who mostly works on the bench, but I love the feeling of power and satisfaction that being a 'computer person' in a molecular biology lab brings. Although it all started with curiosity, it ended up playing a big part in who I am as a scientist. Everything is not about getting work done though. It is also about satisfying my curiosity and keeping me engaged. I need to be always doing something new for my mental well being (I'm the kind of person who will spend a week automating something which could be manually done in a day).

Things I love just because:

  • Indian classical music
  • Bioinformatics, Linux, and computers in general
  • Mass spectrometry of RNA and protein modifications
  • African cichlids and fishes in general

    • This blog is a record of my explorations, with the hope that someone out there finds it useful (or interesting). What follows is filler text.

    R code for Logolas
    

          BiocManager::install("Logolas")
          library(Logolas)
          sequence <- c("CTATTGT", "CTCTTAT", "CTATTAA", "CTATTTA", "CTATTAT", "CTTGAAT",
                        "CTTAGAT", "CTATTAA", "CTATTTA", "CTATTAT", "CTTTTAT", "CTATAGT",
                        "CTATTTT", "CTTATAT", "CTATATT", "CTCATTT", "CTTATTT", "CAATAGT",
                        "CATTTGA", "CTCTTAT", "CTATTAT", "CTTTTAT", "CTATAAT", "CTTAGGT",
                        "CTATTGT", "CTCATGT", "CTATAGT", "CTCGTTA", "CTAGAAT", "CAATGGT")
          # Plot regular logo
          logomaker(sequence, type = "Logo")
          # Plot ED logo
          logomaker(sequence, type = "EDLogo")
          # Get the actual PWMs
          logomaker(sequence, type = "EDLogo", return_heights = TRUE)
          # Custom colors
          logomaker(sequence, color_type = "per_row",
                    colors = c("#7FC97F", "#BEAED4", "#FDC086", "#386CB0"),
                    type = "EDLogo")
          # User supplied background values
            # default bg is NULL where all letters are equal probability
          bg <- c(0.05, 0.90, 0.03, 0.05)
          names(bg) <- c("A", "C", "G", "T")
          logomaker(sequence, bg=bg, type = "EDLogo")
          # Adaptive scaling depending on number of alignments (dash - https://github.com/kkdey/dashr)
          logomaker(sequence, use_dash = FALSE, type = "Logo",
                    logo_control = list(pop_name = "use_dash = FALSE"))
          logomaker(sequence, type = "Logo", logo_control = list(pop_name = "use_dash = TRUE"))
          # Get consensus logo - lower case=disfavoured/lowest freq
          GetConsensusSeq(sequence)