| package main | |
| import ( | |
| "fmt" | |
| "math" | |
| "gonum.org/v1/gonum/stat/distuv" | |
| ) |
| name: so-ipopt | |
| channels: | |
| - conda-forge | |
| - defaults | |
| dependencies: | |
| - pyomo | |
| - ipopt |
| name: foo | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| dependencies: | |
| - _libgcc_mutex=0.1=conda_forge | |
| - _openmp_mutex=4.5=1_gnu | |
| - _r-mutex=1.0.1=anacondar_1 | |
| - binutils_impl_linux-64=2.35=h18a2f87_9 |
| name: so-seurat | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| dependencies: | |
| - _r-mutex=1.0.1=anacondar_1 | |
| - bwidget=1.9.14=0 | |
| - bzip2=1.0.8=haf1e3a3_3 | |
| - c-ares=1.16.1=haf1e3a3_3 |
| #!/usr/bin/env awk -f | |
| #' Author: Mervin Fansler | |
| #' GitHub: @mfansler | |
| #' License: MIT | |
| #' | |
| #' Basic usage | |
| #' $ conda list --export | awk -f list_export_to_yaml.awk | |
| #' | |
| #' Omitting builds with 'no_builds' | |
| #' $ conda list --export | awk -v no_builds=1 -f list_export_to_yaml.awk |
SAM and BAM filtering one-liners
@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please extend with additional/faster/better solutions via a pull request!
BWA mapping (using piping for minimal disk I/O)
| name: kallisto-build | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| dependencies: | |
| - autoconf | |
| - automake | |
| - hdf5 | |
| - make |
| name: genewalk | |
| channels: | |
| - bioconda | |
| - conda-forge | |
| - defaults | |
| dependencies: | |
| - pandas | |
| - networkx>=2.1 | |
| - gensim | |
| - goatools |
| library(tidyverse) | |
| # values at which to evaluate | |
| # this can be changed arbitrarily | |
| x <- c(1,2,3) | |
| # evaluate y's for every condition and output a long format table | |
| df <- expand.grid(coef=c(1,2), pow=c(1,2,3)) %>% | |
| group_by(coef, pow) %>% | |
| mutate(y=map2(coef, pow, ~ tibble(x=x, y=.x*x^.y))) %>% |
| #!/usr/bin/env bash | |
| # Example Usage | |
| # ./extract_10X_cell.sh possorted_genome_bam.bam GCCAAATTCACATACG | samtools view -b > cell.bam | |
| # | |
| # Compare with 10X post: | |
| # https://kb.10xgenomics.com/hc/en-us/articles/360022448251-Is-there-way-to-filter-the-BAM-file-produced-by-10x-pipelines-with-a-list-of-barcodes- | |
| if [ "$#" -ne 2 ]; then | |
| echo -e "Incorrect number of parameters! Usage:\n extract_10X_cell.sh <file.bam> <cell_bx>" >&2 |
