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Single Cell Biology

Avi Srivastava k3yavi

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Single Cell Biology
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import sys
##########################################################
#requires snakemake, python3, pyfasta to be installed
#save this file and provide all the binaries and their path
#in variables below.
#to run flux pipeline:
#snakemake run_flux_pipeline
#to run rsem pipeline:
#snakemake run_rsem_pipeline
```
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 "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install)"
brew install zsh
@k3yavi
k3yavi / spacemacs-cheatsheet.txt
Last active February 28, 2024 01:15 — forked from davoclavo/spacemacs-cheatsheet.md
Spacemacs cheatsheet
//from http://www.saltycrane.com/blog/2015/12/switching-emacs-vim-actually-spacemacs/
Useful Spacemacs commands
SPC q q - quit
SPC w / - split window vertically
SPC w - - split window horizontally
SPC 1 - switch to window 1
SPC 2 - switch to window 2
SPC w c - delete current window
https://www.youtube.com/watch?v=F0sRpgnFyMY
## Evil mode
/ Start search in current buffer
n find next
N find previous
SPC s c clear the searches
:s/text/newtext/gc Search and replace
SPC s h Symbol highlight + options for search, multiple edit,...
ALL = alevin.pdf
TEXFILES = alevin
# STYFILES = our-comments
CLSFILES = bmcart
FIGURES = figs/alevin.pdf figs/timing.pdf
LATEXMKOPTS = -pdf -dvi-
LATEX = pdflatex
BIBFILES = bmc_article
########### Shouldn't require configuration below here ##########
@k3yavi
k3yavi / alevin-default.ipynb
Last active July 11, 2019 20:35
Example pipeline for Alevin-tool on 10x-pbmc 1k data.
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@k3yavi
k3yavi / merge.ipynb
Last active October 27, 2018 20:07
Depth Normalization of Alevin generated counts on multiple libraries.
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@k3yavi
k3yavi / go_analysis.ipynb
Created February 2, 2019 03:51
Go analysis in R
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DATASETS = ["PBMC_8K", "PBMC_4k"]
SALMON = "$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",