semvec/pypi-packages huggingface dataset:
TopDownCrawl 1.0.1
TopDownCrawl is a tool for aligning quantitative binding data for k-mers from experiments such as SELEX-seq and SMiLE-seq

# TopDownCrawl

Top-Down-Crawl is able to rapidly align quantitative binding data from experiments such as SELEX-seq and SMiLE-seq. Methods like these are able to provide highly reprodible k-mer level measurements of binding affinity, but understanding where an enriched k-mer falls along the bidning site depends on alignment. k-mer level data is more informative than simplistic PWM-based models which assume independent contributions between positions of the binding site.

The python script (TDC.py) accepts a table (.txt, .tsv, .csv, .xlsx, .xls) as input including the sequences in column 1, and the associated binding measurements in column 2. Values for reverse complements will be averaged if provided, or assumed to be equivalent if not. The first row is expected to contain header names of your choosing. An example input file is included (example_MEF2B_R1_E_k7.tsv).


### STEP 1: Install Package with Dependencies

`pip install TopDownCrawl`

### STEP 2: Run Top-Down Crawl
```
# Accepted formats (.txt, .tsv, .csv, .xlsx, .xls)
TopDownCrawl <input>

ie: TopDownCrawl MEF2B_R1_k7_enrichment.tsv (can be found in example folder)
```

### OUTPUT
```
# Aligned and reverse-complement-averaged input (tab-delimited)
<input>_aligned.tsv

# Show how many sequences align to each shift
<input>_summary.tsv    

# Position weight matrix (PWM) of the aligned input, weighting each sequence by its associated binding metric, removing the 2 most extreme shifts 
<input>_PWM.png        

# Position weight matrix (PWM) of the aligned input, weighting each sequence by its associated binding metric, removing the 2 most extreme shifts 
<input>_PWM_rc.png
```
repl-uploader 2.2.7
Collection of scripts to upload Replicon expenses

## Synopsis

This is a simple code to extract data information from an excel (with a predefined format) and send it to a new Replicon expense sheet using webservices.

## Motivation

Simplify my expenses reports

## Installation

1. Install Python - https://www.python.org/downloads/ (I am using python 3.8)

2. Check if python is in the path environment variable

    a) Command+r > type "rundll32 sysdm.cpl,EditEnvironmentVariables"

    b) Check if there is somenthing like "C:\Program Files (x86)\Python37-32\scripts;C:\Program Files (x86)\Python37-32" in the PATH variable

    c) Add it if necessary

3. Open a command window and install the required python modules using the following command:
```
pip install repl_uploader
```

4. Install de xlwings addon on excel typing the following command on a command window:
```
xlwings addin install
```

5. Garantee that the Project Name Format in your replicon is set to "Name - Code"

	a) Login on your Replicon account
	
	b) Go to settings (engine wheel - upper right corner)
	
	c) Change "Project Name Format" to "Name - Code"

6. When a new release is available, upgrade with the following command:
```
pip install --upgrade repl_uploader
```

## API Reference

xlwings - http://docs.xlwings.org/en/stable/quickstart.html

## Author
* **Thiago Weidman**

## Contributors
* **Danilo Passos** - The guy who made the worksheet template (Yeap, I stole the idea).
* **Rodrigo Tomazeli** - The Beta tester and "implementer"
* **Manuel Cardoso** - The new features specifier :)