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applyfunctionsr

how to use apply functions in R

brocc

Consensus taxonomy assignment for short reads (great for fungi)

brocccontig

use of BROCC for long PacBio contigs for taxonomy annotation

cancergenelist

maintain the list of cancer-associated genes

cdd_cluster

custom annotation to cdd hits

cellclassgenomicfeatures

Cell class genomic and epigenetic features for Lineage Tracing

choose

several implementations of binomial coefficient calculation: choose(n, k)

citationextract

get abstracts and refs from PubMed and reformat them

contigannotation

diffblast

find number of reads that align for one BLAST db but not other

extractgenomeannotation

extract genome annotation for human, mice and gorilla genomes and reformat it

fasta_processing

how to process FASTA files in Python, R and bash

filterfasta

filter FASTA file based on sequence identifier and extract subsequences from start to end position

gccontent

calculate GC percentage for reference genomes with multiple windows

genomedepth

average genome depth, depth distribution and coverage

hiannotator

Functions for annotating GRanges objects

linearmodelsintro

simple description of lm() function in R

motif_seach_example

how to use Biostrings to find patterns

ngram

generate n-grams and frequencies

prefixfasta

add prefix to fasta identifier

qiimemap

aux scripts to work with qiime map and metadata files

qiimer

Quantitative Insights Into Microbial Ecology - parsing and plotting functions for R

seq_uniq

extract unique and similar sequences

sitesforpatient

For a given Patient and (optionally) timepoint and celltype get unique sites and metadata

textsubstitution

perform substitutions on the original text based on set of rules

titanicviz

Sample Shiny App