| import numpy as np | |
| import pandas as pd | |
| import seaborn as sns | |
| from scipy.signal import find_peaks | |
| import matplotlib as mpl | |
| import matplotlib.pyplot as plt | |
| import scanpy as sc | |
| from anndata import AnnData |
Best way to set this up is to install opam (the ocaml package manager) For the current (2024-06-23) version of googledrive ocaml fuse (0.7.32), you can't use the latest version of opam because it uses old packages.
sudo bash -c "sh <(curl -fsSL https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh)"
Then run
| chrom chromStart chromEnd name gieStain | |
| chr1 0 2300000 p36.33 gneg | |
| chr1 2300000 5300000 p36.32 gpos25 | |
| chr1 5300000 7100000 p36.31 gneg | |
| chr1 7100000 9100000 p36.23 gpos25 | |
| chr1 9100000 12500000 p36.22 gneg | |
| chr1 12500000 15900000 p36.21 gpos50 | |
| chr1 15900000 20100000 p36.13 gneg | |
| chr1 20100000 23600000 p36.12 gpos25 | |
| chr1 23600000 27600000 p36.11 gneg |
| """Python script to spoof metadata to converted tiff files | |
| This script adds necessary metadata to images converted from tif/jpg/png and are not compatible with openslide format. Using the tifftools library, we can spoof the metadata to make it compatible with openslide or other image processing libraries. This script is created using the guide from http://www.andrewjanowczyk.com/converting-an-existing-image-into-an-openslide-compatible-format/ | |
| This script requires the following packages: | |
| - argparse | |
| - tifftools | |
| You need to specify the power and microns per pixel for all images, run them separately if you have different specifications for different images. | |
| """ |
(Tested on Manjaro, Ubuntu 18.04, Ubuntu 20.04)
Our school uses the L2TP/IPsec with PSK protocol, and I've read plenty of stackexchage and forum posts regarding issues with setting up L2TP/IPsec on a Linux system. After many trials and errors I managed to set it up, and helped friends and colleagues who use Linux as their PC. I haven't shared or replied to any threads about the solution I found, primarily because I don't really know why the other methods didn't work and why this setting in particular works 🤷 So here we go.
I am going to set this up with the GUI Networkmanger, which should be installed on your MANJARO distro by default, if not, run
sudo pacman -S NetworkManager
Next, open up your Networkmanager by Systems Settings > Network - Connections
| # function to retreive KEGG pathway names from KEGGREST. For some strange reasons, they won't take a list of queries even though the query size was set at 100. However, when I execute the query one path at a time, I would get an error message saying "Forbidden (HTTP 403)", hence the sys.sleep break. I am guess querying more than 100 within a short period of time would not be allowed too. I'm expecting a KEGGgraph input of graphs with path ID that are like "X00010", but feel free to remove the gsub function if you have already formatted your pathID into the "map00010" form. | |
| library(KEGGREST) | |
| kegg_all_names <- function(pathID) { | |
| repeats <- floor(length(pathID) / 100) | |
| final_rep <- length(pathID) %% 100 | |
| pathNames <- NULL | |
| for (i in 1:repeats) { | |
| pathNames <- c(pathNames, unlist(lapply(gsub("X", "map", pathID[(1 + (i * 100) - 100):(i * 100)]), function(x) keggFind("pathway", x)))) |
There are many instances where more than one aliquot is provided by TCGAbiolinks datasets, but you will only need one of those. In this case, GDC has offered a standard set of Replicate Sample rules to select the most 'scientifically advantageous' aliquot for study.
From the GDC Documentation Encyclopedia
| #' filter_replicate_samples | |
| #' | |
| #' Function to filter technical replicates in TCGA samples | |
| #' Doc: https://gist.github.com/alexllc/8dcd229ed3ad7f069e92dc30d5eac83a | |
| #' | |
| #' @source \url{http://gdac.broadinstitute.org/runs/stddata__2014_01_15/samples_report/READ_Replicate_Samples.html} | |
| #' @param bcr list of barcodes | |
| #' @param verbose print out which barcodes are kept and which ones are filtered | |
| #' | |
| #' @return subset of the list of barcodes |