Skip to content

Instantly share code, notes, and snippets.

View sr320's full-sized avatar

Steven Roberts sr320

77 followers · 53 following
View GitHub Profile
@sr320
sr320 / Olurida-papers.md
Last active April 25, 2023 11:47
Olympia Oyster Papers
@sr320
sr320 / keybase.md
Created January 11, 2021 18:46

Keybase proof

I hereby claim:

  • I am sr320 on github.
  • I am sr320 (https://keybase.io/sr320) on keybase.
  • I have a public key ASBwRjGw-qF_63Uf7zPuZ2PC-6kxek-eViLk3WskPrTk7Ao

To claim this, I am signing this object:

@sr320
sr320 / gist:f11553a40bcb1fb6f38ae100f8b3b379
Created February 15, 2017 00:00
021417-abacus-stdout.txt
steven@emu:~/bioinfo/021417$ java -Xmx16g -jar /home/shared/abacus/abacus.jar -p \
> Abacus-01.param
***********************************
Abacus
Version: 2.5
***********************************
Developed and written by: Damian Fermin and Alexey Nesvizhskii
Copyright 2010 Damian Fermin
@sr320
sr320 / gist:0cb40491f8542f361b2c2484480554dd
Created February 15, 2017 00:00
021417-abacus-stdout.txt
steven@emu:~/bioinfo/021417$ java -Xmx16g -jar /home/shared/abacus/abacus.jar -p \
> Abacus-01.param
***********************************
Abacus
Version: 2.5
***********************************
Developed and written by: Damian Fermin and Alexey Nesvizhskii
Copyright 2010 Damian Fermin
@sr320
sr320 / gist:3f60b50fae9feca1dbc26b387e587ec8
Created February 15, 2017 00:00
021417-abacus-stdout.txt
steven@emu:~/bioinfo/021417$ java -Xmx16g -jar /home/shared/abacus/abacus.jar -p \
> Abacus-01.param
***********************************
Abacus
Version: 2.5
***********************************
Developed and written by: Damian Fermin and Alexey Nesvizhskii
Copyright 2010 Damian Fermin
@sr320
sr320 / xinteract_readme.md
Created February 10, 2017 14:55
xinteract_readme 
 /usr/tpp_install/tpp/bin/xinteract
 /usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64))
 usage: xinteract (generaloptions) (-Oprophetoptions) (-iiprophetoptions) (-Mptmprophetoptions) (-Xxpressoptions) (-Aasapoptions) (-L<conditionfile>libraoptions) xmlfile1 xmlfile2 ....

 generaloptions:
            For developers:
                 -t  [run regression test against a previously derived result]
                 -t! [learn results for regression test]
                 -t# [run regression test, do not stop on test failure]
@sr320
sr320 / lncRNA-blastn-Ssalar-v1.ipynb
Created May 11, 2016 16:42
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@sr320
sr320 / From-Ensenada.md
Last active November 17, 2015 01:26
Notebook post on panopea project

There have not been many posts recently, but that is not to say I have not been doing any science. Much of what I have been doing is numerous burst commits on the Panopea transcriptome paper / project. This can be found @ https://github.com/sr320/paper-pano-go.

You can see all the Jupyter nbs in this sub-directory. I will highlight some of my proudest cell moments here:

Ok the first one is so good I will just give you the whole thing except that I will provide just a little more comments ##

!wc -l analyses/Geoduck-transcriptome-v2.tab
@sr320
sr320 / gist:491e9d618aa4699ec3fc
Created February 5, 2015 17:51
Stacks on hummingbird
This file has been truncated, but you can view the full file.
{
"metadata": {
"name": "",
"signature": "sha256:43e451368edace0e55cb05d7b11cb77dfffa12b132a73a6993fbf7eaeee0826c"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
@sr320
sr320 / gist:7196b3d440d40c6fcb9a
Created February 2, 2015 19:23
BiGo: examining statistical differences in two TE subtypes (repeats and wublastx targets)
{
"metadata": {
"name": "",
"signature": "sha256:6a2c4937c9f7b56d5a87f63f909673244ddf55041c4a61246dc2d1054b142b7d"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [