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Isaac Virshup ivirshup

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ivirshup / featureCount_stats.txt
Created Oct 12, 2016
featureCount$stats from running Rsubread multiple times with R v3.3.1 and Rsubread v1.22.3. R was compiled with gcc v4.4.7.
View featureCount_stats.txt
Status SRR950078 SRR950079 SRR950080 SRR950081 SRR950082 SRR950083 SRR950084 SRR950085 SRR950086 SRR950087
1 Assigned 771600 758170 771620 782006 709176 769418 762469 775637 817422 811414
2 Unassigned_Ambiguity 0 0 0 0 0 0 0 0 0 0
3 Unassigned_MultiMapping 0 0 0 0 0 0 0 0 0 0
4 Unassigned_NoFeatures 143539 140245 137103 142209 129824 146504 131665 144008 107762 122946
5 Unassigned_Unmapped 81716 98620 88046 72146 157535 80385 102452 76928 71142 62661
6 Unassigned_MappingQuality 3145 2965 3231 3639 3465 3693 3414 3427 3674 2979
7 Unassigned_FragmentLength 0 0 0 0 0 0 0 0 0 0
8 Unassigned_Chimera 0 0 0 0 0 0 0 0 0 0
9 Unassigned_Secondary 0 0 0 0 0 0 0 0 0 0
View download_conquer.py
from subprocess import run, PIPE
import requests
import pandas as pd
from pathlib import Path
BASE_URL = "http://imlspenticton.uzh.ch/robinson_lab/conquer/"
def curl(inpth, outpth=None):
command = ["curl", str(inpth)]
if outpth:
@ivirshup
ivirshup / gen_h5ad.py
Created May 4, 2018
scanpy scaling issue
View gen_h5ad.py
import matplotlib
matplotlib.use('Agg') # plotting backend compatible with screen
import scanpy.api as sc
from argparse import ArgumentParser
sc.settings.verbosity = 4 # show logging output
def main():
parser = ArgumentParser(
description="Reads in 10x hdf5 file and write a h5ad file.")
@ivirshup
ivirshup / mean_var_test.py
Created May 28, 2018
Profiling memory usage of `scanpy`'s `_get_mean_var`.
View mean_var_test.py
import scanpy
import scanpy.api as sc
import numpy as np
from scipy import random, sparse
from time import sleep
import sklearn.utils.sparsefuncs as sparsefuncs
@profile
def current_dense(X):
return scanpy.preprocessing.simple._get_mean_var(X)
@ivirshup
ivirshup / hv_coloring.py
Created Sep 4, 2018
Switching between categorical and continuous Dynamic Map coloring (not working)
View hv_coloring.py
import holoviews as hv
import numpy as np
import pandas as pd
hv.extension("bokeh")
# Generate data
base_df = pd.DataFrame({
"x": np.random.randn(100), "y": np.random.randn(100),
"cat1": np.random.randint(0, 5, 100), "cat2": np.random.randint(0, 5, 100),
"con1": np.random.randn(100), "con2": np.random.randn(100)})
@ivirshup
ivirshup / centos6_environment.yml
Created Oct 12, 2018
Scanpy scatter plotting circles
View centos6_environment.yml
name: scanpy_scatter_ring
channels:
- defaults
- r
- bioconda
- conda-forge
dependencies:
- anndata=0.6.10=py_0
- igraph=0.7.1=hcc8e21d_5
- louvain=0.6.1=py36hfc679d8_1
@ivirshup
ivirshup / Pipfile.lock
Created Oct 24, 2018
scanpy_pipfile 12:42:35 PM Oct 24, 2018
View Pipfile.lock
{
"_meta": {
"hash": {
"sha256": "aa4e26d643aa1ae7337e67cf9da430773141ac3e9930891ae0862d948e73b6d5"
},
"pipfile-spec": 6,
"requires": {
"python_version": "3.6"
},
"sources": [
@ivirshup
ivirshup / ids_as_index.py
Created Feb 14, 2019
Set `adata.var_names` to be ids not names. Based on default reading of 10x h5 files
View ids_as_index.py
def fix_names(adata):
adata.var_names_make_unique()
adata.var["gene_symbols"] = adata.var.index
adata.var.index = adata.var["gene_ids"]
@ivirshup
ivirshup / download_expression_atlas.py
Created Feb 17, 2019
Get AnnData from expression atlas
View download_expression_atlas.py
import anndata
from scipy import sparse
import pandas as pd
import numpy as np
from pathlib import Path
from tqdm import tqdm
from urllib.request import urlretrieve
from zipfile import ZipFile
@ivirshup
ivirshup / download_expression_atlas.py
Last active Feb 17, 2019
Get AnnData from expression atlas
View download_expression_atlas.py
import anndata
from scipy import sparse
import pandas as pd
import numpy as np
from pathlib import Path
from tqdm import tqdm
from urllib.request import urlretrieve
from zipfile import ZipFile