Avi Srivastava k3yavi
k3yavi
/ upload_to_zenodo.py
Created
October 30, 2019 23:25
— forked from rob-p/upload_to_zenodo.py
Upload a local file to a zenodo deposition
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import requests | |
| import argparse | |
| import pprint | |
| import os | |
| def do_upload(args): | |
| ACCESS_TOKEN = args.token | |
| depid = args.deposition_id | |
| url = 'https://zenodo.org/api/deposit/depositions/{}'.format(depid) | |
| r = requests.get(url, params={'access_token': ACCESS_TOKEN}) |
k3yavi
/ alevin.snk
Created
June 7, 2019 17:12
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| DATASETS = ["PBMC_8K", "PBMC_4k"] | |
| SALMON = "$BINS/salmon-0.14.0_linux_x86_64/bin/salmon" | |
| rule all: | |
| input: expand("quants/{dataset}/alevin/quants_mat.gz", dataset=DATASETS) | |
| rule salmon_quant: | |
| input: | |
| r1 = "reads/{sample}_1.fastq", |
k3yavi
/ loading.ipynb
Created
February 7, 2019 23:31
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
k3yavi
/ merge.ipynb
Last active
October 27, 2018 20:07
Depth Normalization of Alevin generated counts on multiple libraries.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
k3yavi
/ alevin-default.ipynb
Last active
July 11, 2019 20:35
Example pipeline for Alevin-tool on 10x-pbmc 1k data.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ALL = alevin.pdf | |
| TEXFILES = alevin | |
| # STYFILES = our-comments | |
| CLSFILES = bmcart | |
| FIGURES = figs/alevin.pdf figs/timing.pdf | |
| LATEXMKOPTS = -pdf -dvi- | |
| LATEX = pdflatex | |
| BIBFILES = bmc_article | |
| ########### Shouldn't require configuration below here ########## |
k3yavi
/ spacemacs-keybindings.txt
Created
May 16, 2017 23:12
— forked from Softsapiens/spacemacs-keybindings.txt
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| https://www.youtube.com/watch?v=F0sRpgnFyMY | |
| ## Evil mode | |
| / Start search in current buffer | |
| n find next | |
| N find previous | |
| SPC s c clear the searches | |
| :s/text/newtext/gc Search and replace | |
| SPC s h Symbol highlight + options for search, multiple edit,... |
k3yavi
/ spacemacs-cheatsheet.txt
Last active
August 14, 2024 21:24
— forked from davoclavo/spacemacs-cheatsheet.md
Spacemacs cheatsheet
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| //from http://www.saltycrane.com/blog/2015/12/switching-emacs-vim-actually-spacemacs/ | |
| Useful Spacemacs commands | |
| SPC q q - quit | |
| SPC w / - split window vertically | |
| SPC w - - split window horizontally | |
| SPC 1 - switch to window 1 | |
| SPC 2 - switch to window 2 | |
| SPC w c - delete current window |
k3yavi
/ Non-admin Installs
Last active
June 21, 2016 20:13
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ``` | |
| wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh | |
| chmod +x Miniconda3-latest-Linux-x86_64.sh | |
| ./Miniconda3-latest-Linux-x86_64.sh | |
| #<Might have to write Yes and press enter> | |
| ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install)" | |
| brew install zsh |