Ramon Fallon Code (rafalcode)
- Why the medieval man counting stars woodcut logo? Let's take that in parts ("divide and conquer"): Why the counting? The Irish for computer is "riomhair" (counter) which is where computers started and it's still largely true about their fundamental role. Medieval man? This epoch is widely regarded as having made no progress, but certain fundamentals were established: the rise of learning in monasteries, Ockham's Razor and the collation and curation (preservation) of previous knowledge from Antiquity.
- All repositories are so called "proof of concept", and not in any ways production-level, so that no there no self standing projects.
- Nevertheless some can be used are components of projects and can sometimes be compiled as utility tools.
- As an "early days" linux user and programmer, there is a good deal of C and shell, but also python and R reflecting recent experience as a bioinformatician.
- My R Shiny apps are hosted at https://shiny.dna.ovh/users/ramon.
1. adna
A simple django website which gives the system time for the system running the site, repo here.
2. awkplay
Various scripts for handled table like data using this venerable old program, repo here.
3. bibida
Advice, tools and scripts for handling large bioinformatics data files, repo here.
4. cairims
I love the Cairo graphics library. It's become a staple internal tool of many other programs. Several snippets here for generating images, repo here.
5. bioperling
Using the Bioperl Perl library for bioinformatics. The biopython library is built very similarly, repo here.
6. chin_resto
The Chinese restaurant process is an intriguing random process, particularly because it leads off a very simply described principle, repo here.
7. cregexinaction
Using the C library for regular expressions, repo here.
8. cppwha
Short for "C++ what?", small C++ snippets, repo here.
9. wavchudit
For audio wav files, breaking them into chunks and usually putting these into to subfolder. Useful for breaking down large audio files. Mplayer's EDL format accepted. repo here.
10. fnjungle
File name jungle, script for solving problems with dodgy filenames, repo here.
11. fortranstateofmind
Swanky name for very some simple fortran programs , repo here.
12. gd_png_ex
Mostly PNG library manipulation mini-programs , repo here.
13. htslib
Fork of HTS library, part of samtools, raw bioinformatic data file proessing , repo here.
14. imagcli
Imagemagick Command-line scripts, repo here.
15. juegooca
Somewhat cryptic name for what I call an occurence counter. Given a vector random (often repeating) integers, print out how many times (and in what positions) each occurence of vector has been found. Hashes are not used, making this more suitable to smaller vectors. So I used the abbrevation "oc" for occurence, and as it felt like a game, I remember Spanish children have a game called "El juego de la Oca", so I called the repo: "juegooca"!. Repo here.
16. klib
Fork, a promising graphics library for C, repo here.
17. kmeanscode
One of the classic algorithms: rendering data into K groups based on means/centroids. I'm attached to Hartigan's method and his Urns book, repo here.
18. kplot
A simple , repo here.
19. layoutim
Simple image layoutsLaying out images, repo here.
20. lda-c
Fork of the Latent Dirichlet method of categorising texts. Repo here.
21. libharudemos
A simple , repo here.
22. libjp
Using the JPEG library for editing JPG images en masse, repo here.
23. libplinkio
Plink library usage, repo here.
24. libsslprogs
SSL library usage, repo here.
25. MACS
Fork of the ChIP-Seq peak finder program, MACS, repo here.
26. mlelr
Fork of Scott Czepiel's logistic regression program done in C with GSL library. Although I dislike having dependencies, Scott gives a convincing reason for why sometimes they are necessary. Repo here.
27. mpifast
A simple , repo here.
28. mreps
A simple , repo here.
29. msms
Fork and re-renderer of Hudson's classic MS simulator, repo here.
30. murmur3
Fork, repo here.
31. ngsLD
Fork, link desequilibrium in NGS, repo here.
32. nxtflo
Some very elementary nextflow (bioinformatics pipeline) scripts, repo here.
33. orgops
A simple , repo here.
34. osTicket-1.8
Outdated (from 2016) fork of the trouble tikecting software, repo here.
35. pafq
A simple , repo here.
36. pgf
A simple , repo here.
37. phase
Fork of Matthews Stephens phasing (haplotype estimation) program, repo here.
38. phylineib
A simple , repo here.
39. phyliptamer
An attempt at taming the PHYLIP phylogenetics program, repo here.
40. pit2f
Pits two files against each other, this is another hashless matcherhere.
41. plplotex
A simple , repo here.
42. pngsim
Simulating png files, repo here.
43. pollsa
Django example, repo here.
44. pollsa0
Django example, repo here.
45. pollsapi
Django canonical polls example, repo here.
46. prokka
Fork, repo here.
47. pwise
Pariwsie comparisons, repo here.
48. r-fresh
Refreshing your R, many protype scripts, repo here.
49. rafalcode.github.io
HTML for this github.io page, repo here.
50. ratemats
A simple , repo here.
51. rblog2
A simple , repo here.
52. reg-gen
A simple , repo here.
53. rf717
EBI Exercise, repo here.
54. Roary
Fork, repo here.
55. rscripting
Simple R scriptshere.
56. rstuff
Various R scripts, repo here.
57. seego
First steps int he go programming language, repo here.
58. sickle
Trimming NGS reads, repo here.
59. simicoal
Simualtion of the coalescent, repo here.
60. simupopex
Simulating populations, repo here.
61. sox
Fork of the audio processing programi, repo here.
62. srst2
My small contribution to Kat Holt's codehere.
63. stkprac
A simple , repo here.
64. strgarrman
A simple , repo here.
65. tenugg
A simple , repo here.
66. txform
A simple , repo here.
67. typigwal
A simple , repo here.
68. vardocs
A simple , repo here.
69. vim-mediawiki-editor
A simple , repo here.
71. wtosc
Simple wavetable oscillator, repo here.
72. xlpa
A simple , repo here.
73. xpehh
Forked and parallelised (via openmp) xpehh program, repo here.