| $ git clone https://github.com/goodarzilab/lorna-sh | |
| $ cd lorna-sh | |
| ## look around...i decided to try starting in processing_seqs | |
| $ find . | |
| $ cd processing_seqs | |
| ## in R repl, install dependencies | |
| ## data.table | |
| ## optparse |
here is a picture of a "RNA-seq BAM file" in JBrowse 2
you can see that there are all these little grey boxes and the black lines connecting them. These are the so-called "reads" in the RNA-seq BAM file! there is also a little "histogram" along the top. This is showing how many "reads" mapped to a given position in the genome
| ## step 1, get miniconda | |
| ./Miniconda3-latest-Linux-x86_64.sh # follow a bunch of y/n questions in here | |
| ## for me, i did not activate it by default so i manually activate it like this in zsh shell | |
| eval "$(/home/cdiesh/miniconda3/bin/conda shell.zsh hook)" | |
| ## then activate environment | |
| conda create -n tf2_10 python=3.9 | |
| conda activate tf2_10 |
| ~/Downloads ❯❯❯ eval "$(/home/cdiesh/miniconda3/bin/conda shell.zsh hook)" | |
| (base) ~/Downloads ❯❯❯ conda activate tf2_10 ✘ 1 | |
| (tf2_10) ~/Downloads ❯❯❯ python3 -m pip install tensorflow==2.10 numpy==1.24 | |
| Collecting tensorflow==2.10 | |
| Using cached tensorflow-2.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.1 kB) | |
| Collecting numpy==1.24 | |
| Using cached numpy-1.24.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB) | |
| Collecting absl-py>=1.0.0 (from tensorflow==2.10) |
| ~/Tiberius ❯❯❯ python3 -m venv .venv ✘ 130 | |
| ~/Tiberius ❯❯❯ .venv/bin/activate | |
| zsh: command not found: .venv/bin/activate | |
| ~/Tiberius ❯❯❯ source .venv/bin/activate ✘ 127 | |
| (.venv) ~/Tiberius ❯❯❯ pip install tensorflow_probability==0.18.0 transformers pyBigWig bio scikit-learn biopython bcbio-gff requests | |
| Collecting tensorflow_probability==0.18.0 | |
| Downloading tensorflow_probability-0.18.0-py2.py3-none-any.whl.metadata (13 kB) | |
| Collecting transformers | |
| Downloading transformers-4.44.2-py3-none-any.whl.metadata (43 kB) | |
| Collecting pyBigWig |
| // usage: | |
| // download this file to a file unprepare_seqs.js | |
| // then run: | |
| // node unprepare_seqs.js /path/to/seq/dir output_file.fa | |
| // after that, fold the lines to a constant line length with: | |
| // fold output_file.fa > output_file2.fa | |
| const fs = require('fs') | |
| const path = require('path') | |
| const dir = process.argv[2] || '.' | |
| const output = process.argv[3] || 'out.fa' |
| #!/bin/bash | |
| # gen_data.sh | |
| # tags.txt is a list of git tags for a repo | |
| cat tags.txt|while read p; do | |
| ## visit our specific JBrowse URL containing tag name in URL | |
| echo -n "$p"$'\t'; node get_page_size.js "https://jbrowse.org/code/jb2/$p/?config=test_data%2Fvolvox%2Fconfig.json&session=share-9NPMoB3dtz&password=aCI2W"; | |
| done; |
| Tomasz Bednarczyk - I see you (Official Video) 2006 https://www.youtube.com/watch?v=lOx6fqT7Cys | |
| Emily Berregaard - A Poem [Strange Rules] https://www.youtube.com/watch?v=liW_749IQ1U& | |
| Olympisk Løft - Tvillingeseglet (Full Album) [Janushoved] 2017 https://www.youtube.com/watch?v=-nMN7ZlUEj8 | |
| angelo harmsworth and theodore cale schafer https://www.youtube.com/watch?v=60UiqNli2vs | |
| the yellow book https://www.youtube.com/watch?v=21S18AxFbjg |
| #!/usr/bin/env Rscript | |
| library(reshape2) | |
| library(ggplot2) | |
| library(tidytext) | |
| x <- read.csv("cpu.csv") | |
| y <- melt(x) | |
| colnames(y) <- c("site", "variable", "s") | |
| y$s <- y$s / 1000 |
| function TranscriptSelector() { | |
| const [error, setError] = useState(); | |
| const [transcripts, setTranscripts] = useState(); | |
| const [selection, setSelection] = useState(); | |
| useEffect(() => { | |
| async () => { | |
| try { | |
| const result = await loadTranscripts(); // imagine this just returned a list of strings | |
| setTranscripts(result); | |
| setSelection(result[0]); // set the initial selection to the first transcript |