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+# bio-aid
+Package containing tools for genetic and genomic analysis in python in the Malkova Lab.
+
+Includes a collection of functions from my other repositories for easier development of new projects
+
+## Installation
+The latest release of the bio-aid package can be installed through pip (https://pypi.org/project/bio-aid/) by using the following command:
+```bash
+pip install --upgrade bio-aid
+```
+bio-aid currently consists of a base module and three sub modules: `deepSeqInsH`, `MMBSearchTK`, `varaintTK`.
+
+To easily import and access the functions inside of the bio-aid package, include the following in your `python` scripts:
+
+```python
+import BioAid as ba
+```
+## Diluter
+This simple program calculates volumes for serial dilutions of yeast cultures, that can subsequently be used for colony plating. To access diluter, in `python` type:
+```python
+ba.dilute()
+```
+and follow instructions on the prompt.
+
+## PopDub
+Utillity for finding population doublings for the Telomere project.
+
+To get results you will need to adjust initial and final population densities:
+- set `initial_population` to the cell count on the beginning of your experiment used as inoculum.
+- set `final_population_ml` to the /ml cell count at the time you want to measure population doublings.
+- set `final_culture_volume` to the volume of your final culture.
+
+Finally, run the function:
+```python
+ba.calculatePopulationDoublings(initial_population, final_population_ml, final_culture_volume)
+```
+## RepeatSearch
+This tool allows for search of imperfect repeats (Inverted and Direct) in a DNA sequence. Diagram explaining the parameters can be found in the stand-alone repo [here](https://github.com/tvarovski/RepeatSearchTools) 
+
+```python
+# Set RepeatSearch parameters
+sequence="ACGT"           # This is your nucleotide sequence to be searched for repeats
+inverted=True             # Sets search to Inverted (True) vs Direct (False) repeats
+min_query_length=5        # Sets min length of a query sequence
+max_query_length=30       # Sets max length of a query sequence
+min_spacer=0              # Set min distance between query and the repeat
+window_size=804           # Sets window size within which the search is confined
+imperfect_homology=True   # Set True/False, to search for imperfect/perfect homologies.
+min_homology=0.8          # Sets minimum homology treshold (a fraction) when imperfect_homology=True,  
+fixed_errors=1            # Sets maximum number of errors (del/sub) when imperfect_homology=True (set to False or to an integer)
+
+# To run the Search execute the following:
+results_dictionary = ba.searchSequenceForRepeats(
+                         sequence=sequence,
+                         min_query_length=min_query_length,
+                         max_query_length=max_query_length,
+                         min_spacer=min_spacer,
+                         window_size=window_size,
+                         imperfect_homology=imperfect_homology,
+                         min_homology=min_homology,
+                         fixed_errors=fixed_errors,
+                         inverted=inverted)
+
+```
+
+