tbrittoborges

#!/bin/bash

if [ $# -ne 1 ]; then
  echo "Usage: $0 <input_gtf_file>"
  exit 1
fi

input_gtf="$1"
output_prefix="output"
sorted_gtf="${output_prefix}.sorted.gtf"

tbrittoborges

#!/bin/bash env

conda activate
mkdir -p envs/.export

PREFIX=$(dirname "$CONDA_PREFIX")

for d in "$PREFIX"/*; do
    BNAME=$(basename "$d")
    echo "$BNAME"

tbrittoborges

library(plyranges)

set.seed(1)
x <- data.frame(seqnames=1, start=0:9 * 100 + 1, 
                width=20, id=1:10) %>%
  as_granges()

y <- data.frame(seqnames=1, start=round(runif(4,100,900)), 
                width=10, id=letters[1:4]) %>%
  as_granges() %>%

tbrittoborges

"""
    This example shows how to use the streaming feature with functions.
"""

import json
import os
import sys
from collections.abc import Generator
from typing import Any, Dict, List

tbrittoborges

library(tidyverse)
library(ggrepel)

# load the data to variable x
x <- read_csv('leafcutter_junctions.csv')

x %>% 
 # filters the dataframe to keep only significant called junctions
 filter(abs(deltapsi) > 0.1 & p.adjust < 0.05) %>% 
 # groups junctions by comparison

tbrittoborges

tbrittoborges

#!/usr/bin/env python
# coding: utf-8
from pathlib import Path
import os
from itertools import chain
from datetime import datetime
__author__: tbrittoborges
__date__: 05/02/2020

tbrittoborges

#!/usr/bin/env python
# coding: utf-8
from pathlib import Path
import os
from itertools import chain
from datetime import datetime
__author__: tbrittoborges
__date__: 05/02/2020

tbrittoborges

(majiq) tbrittoborges@atlas:/prj/CellRNANetworks/Baltica$ majiq build -h
Traceback (most recent call last):
  File "/home/tbrittoborges/miniconda3/envs/majiq/bin/majiq", line 7, in <module>
    from majiq.run_majiq import main
  File "/home/tbrittoborges/miniconda3/envs/majiq/lib/python3.5/site-packages/majiq/run_majiq.py", line 2, in <module>
    from majiq.src.build import build
  File "majiq/src/build.pyx", line 24, in init majiq.src.build
  File "/home/tbrittoborges/miniconda3/envs/majiq/lib/python3.5/site-packages/voila/api/__init__.py", line 1, in <module>
    from voila.api.matrix_hdf5 import Psi, DeltaPsi, Heterogen
  File "/home/tbrittoborges/miniconda3/envs/majiq/lib/python3.5/site-packages/voila/api/matrix_hdf5.py", line 8, in <module>

tbrittoborges

library(tidyverse)

library(lubridate) # for the days() function
library(fuzzyjoin) # for the fuzzy_left_join() function

climate <- read_tsv('./timetable.csv')
#  date         temperature
#1 2018-11-21   100 
#2 2018-11-22    80