Index

Symbols

!= operators " " white space "\l" white space "\n" white space "\r" white space "\t" white space "array coordinates" "cartesian coordinates" # comment % maths & bitwise operators **kwargs .gitignore version control

16S rRNA 3rd party libraries < operators <= operators == operators > operators >= operators @ operators ^ bitwise operators | bitwise operators |Ho| hypothesis testing |pvalue| hypothesis testing

A

add maths version control advanced indexing numpy alignment display variation cogent3 pretty print cogent3 all numpy analytical statistical distributions and logical operator any numpy

app_help() help() arguments function array array comparisons numpy as keyword assert, [1] assignment, [1] immutable indexing, list numpy assignment unpacking, [1] axis numpy

B

b"" str bitwise operators & ^ | bool Falsy Truthy types bool array numpy, [1] boolean indexing numpy

bootstrapping branch length expected number of substitutions, [1], [2] broadcast numpy broadcasting numpy builtin function, zip functions range sum bytes str string

C

C-style str calibration rate matrix ChIP-seq chronological root cis-regulatory module CRM clone version control close files codon cogent3 alignment, display variation alignment, pretty print filter table index column table k-mer motif_len Kolmogorov-Smirnov statistical test KS bootstrap statistical test KS statistical test load from file table make table Mann-Whitney statistical test moltype MW bootstrap statistical test MW statistical test quantiles statistical test cogent3 Alignment slice collection objects dict types list types tuple types

comment # comment lines comment lines comment commit version control comprehension dict list concatenating string conditionals elif else if numpy config version config conflict version control context dependent mutation coordinates plotly correctness count numpy CRM cis-regulatory module

D

data plotly Data Science Debugging a simple Python script using an IDE screencasts decode str, encode string, encode degrees of freedom df hypothesis testing deletion mutation types df hypothesis testing, degrees of freedom dict comprehension plotly types types collection objects

diff version control dir() display variation cogent3 alignment distribution quantile divide maths division remainder maths divmod() maths docstring download data dynamic programming

E

Editing the documents and "make a pull request" screencasts elif conditionals else conditionals empirical statistical distributions empirical distribution encode decode str decode string enumerate loops errors Exceptions escaping characters str

estimate evaluation numpy Exceptions errors KeyError Executing Python from a text file screencasts Executing Python using a REPL screencasts expected number of substitutions branch length, [1], [2] Exploring namespaces using the debugger screencasts exponents maths

F

f-strings str fail test Falsy bool file path files files close file path iterate contents open mode open() writing filter table cogent3 fit a model float types

for loops format str free parameter frozenset type function arguments keyword arguments optional arguments required arguments return syntax zip builtin functions builtin void

G

generator

git version control

H

heigh plotly help() app_help() hints type How to ask for help related to these notes screencasts

hypothesis testing |Ho| |pvalue| degrees of freedom df likelihood ratio LR number of free parameters nfp test statistic

I

if conditionals Immutable immutable, [1] assignment import in logical operator indel insertion deletion mutation types indentation index index column table cogent3 indexing list assignment numpy

insertion mutation types insertion deletion indel install numpy instance int types integer divide maths integer indexing numpy is operators iterate contents files iterator

K

k-mer motif_len cogent3 k-mers KeyError Exceptions keyword as yield

keyword arguments function Kolmogorov-Smirnov statistical test cogent3 KS statistical test cogent3 KS bootstrap statistical test cogent3

L

layout plotly len() Likelihood ratio likelihood ratio LR hypothesis testing list assignment indexing comprehension types collection objects literal string load from file table cogent3 log version control log message version control

log-odds ratios log2 maths maths numpy logical operations numpy logical operator and in or looping range loops enumerate for nested for loop while LR hypothesis testing, likelihood ratio

M

make table cogent3 manifest version control Mann-Whitney statistical test cogent3 marker plotly Markov process stationary stationarity maths % add divide division remainder divmod() exponents integer divide log2 minus modulo operator multiply numpy, log2 plus powers roots subtract matrix numpy matrix multiplication numpy matrix multiply numpy

maximum likelihood maximum likelihood estimators (MLEs) mean numpy merge version control method chaining, [1], [2] methods minus maths module types modules modulo operator maths moltype cogent3 motif motif_len cogent3, k-mer multiply maths mutable mutation context dependent mutation types deletion indel insertion point mutation MW statistical test cogent3 MW bootstrap statistical test cogent3

N

namespace naming variable negative slice nested for loop loops new line string newaxis numpy nfp hypothesis testing, number of free parameters None types notation number of free parameters nfp hypothesis testing numpy advanced indexing all any array comparisons assignment axis bool array, [1] boolean indexing broadcast broadcasting conditionals count evaluation indexing install integer indexing log2 maths logical operations matrix matrix multiplication matrix multiply mean newaxis slicing standard deviation transpose

O

open mode files open() files operators != < <= == > >= @ is

optional arguments function or logical operator

P

parameter pass statement test Paths to files and folders screencasts plotly coordinates data dict heigh layout marker scatter symbol traces width plus maths point mutation mutation types transition transversion

Position Specific Scoring Matrix PSSM Position Specific Weights Matrix PWM powers maths pretty print cogent3 alignment profiles PSSM Position Specific Scoring Matrix pull version control push version control PWM Position Specific Weights Matrix

Q

Q substitution model quantile distribution

quantiles statistical test cogent3

R

r"" str range builtin looping rate matrix calibration substitution model rate parameter raw str Reading a text file using an IDE screencasts repo version control

repository version control required arguments function reset version control residuals return function statement reversed() revert version control roots maths

S

scalar scatter plotly scope screencasts Debugging a simple Python script using an IDE Editing the documents and "make a pull request" Executing Python from a text file Executing Python using a REPL Exploring namespaces using the debugger How to ask for help related to these notes Paths to files and folders Reading a text file using an IDE Substitution models The phylogeny-based maximum likelihood calculation SELEX sequence logo sequence logos set type site slice cogent3 Alignment negative start stop stride, [1] slicing numpy space string stage version control standard deviation numpy standardised residuals start slice statement pass return stationarity Markov process, stationary stationary stationarity Markov process statistical distribution statistical distributions analytical empirical theoretical uniform

statistical power statistical test cogent3, Kolmogorov-Smirnov cogent3, KS cogent3, KS bootstrap cogent3, Mann-Whitney cogent3, MW cogent3, MW bootstrap cogent3, quantiles stop slice str b"" C-style encode decode escaping characters f-strings format r"" raw string formatting string, bytes stride slice, [1] string bytes str concatenating encode decode literal new line space tab types, [1] white space string formatting str string literal substitution matrix substitution model Q rate matrix Substitution models screencasts subtract maths sum builtin symbol plotly syntax function variable

T

tab string table cogent3, filter cogent3, index column cogent3, load from file test fail pass test statistic, [1], [2] hypothesis testing testing TF transcription factor TFBS transcription factor binding site The phylogeny-based maximum likelihood calculation screencasts theoretical statistical distributions theoretical distributions third party libraries time-reversible traces plotly tracked version control transcription factor TF transcription factor binding site TFBS transcription start site TSS transition point mutation transition substitutions

transpose numpy transversion point mutation tree True / False types Truthy bool TSS transcription start site tuple types collection objects type frozenset hints set type casting types type hints type() types types bool collection objects, dict collection objects, list collection objects, tuple dict float int module None string, [1] True / False type casting type()

U

uniform statistical distributions

unpacking unzip, [1]

V

variable naming syntax version config config version control .gitignore add clone commit conflict diff git log log message manifest merge pull push repo repository reset revert stage tracked working copy

void functions

W

while loops white space " " "\l" "\n" "\r" "\t" string

width plotly working copy version control writing files

Y

yield keyword

Z

zip builtin function