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100-shell-script-examples

Collection of shell scripts found on the internet

algorithms_example

List of Algorithms

answers

Random code produced to answer questions on biostars/seqanswers/etc.

apc

(a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join

artificial-neural-networks

asmethodsbenchmarking

Simulated RNAseq data for assessment of differential splicing detection methods.

assemblage

Tools for working with second gen assemblies, fasta sequences, etc

assembly-stats

Assembly statistic visualisation

assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

awesome-spn

A structured list of resources about Sum-Product Networks (SPNs)

benchmarkrna

benchmarkrnaseq

bioawk

BWK awk modified for biological data

biocode

Bioinformatics code libraries and scripts

biostat-578

A repository for all of my teaching material

blacktie

Blacktie: a streamlined interface to the popular tophat/cufflinks RNA-seq pipeline

bootstrap

canu

A single molecule sequence assembler for genomes large and small.

catalog

A dynamic catalog of KBase functionality that can also build/deploy modules automatically

cheatsheets-ai

Essential Cheat Sheets for deep learning and machine learning researchers

chromhmm-enhancers-umel

Identify enhancers. Includes data download, liftover, parallelized workflows, results aggregation, and example output.

coexpression

conda-move

Move environments from an existing conda installation to another directory

contigcount

Example repository created with kb_sdk.

contigfilter

A KBase SDK example module

copycat

Copycat is a simple script to capture and bin the read coverage across a genome from a bam file of read alignments. It relies on bedtools to get coverage for each individual nucleotide in the genome using bedtools genomecov, then bins and organizes these coverage values into 10kb bins and outputs the coverage information in a .csv format (for upload to SplitThreader) and in a .seg format (for viewing the copy number profile in IGV)

data_api

Towards a unified data api for KBase

datasketch

MinHash, LSH, LSH Forest, Weighted MinHash, HyperLogLog, HyperLogLog++

deeplearning-biology

A list of deep learning implementations in biology

dotplotly

Generate an interactive dot plot from mummer or minimap alignments