Welcome!
This is a python repository to generate HCR v3.0 probes for in situ hybridization visualization of mRNA in Anopheles Gambiae. The module allows for quick and easy design of probe pairs for the Hybridization Chain Reaction approach (Choi et al. Development 2018.)
You can install the HCR probe design tool to first create a virtual environment using conda:
conda create --name HCR python=3.10.0
conda activate HCR
You can then use pip to install the HCR probe design tool:
pip install AGambiaeHCRdesign
Dependencies: BLAST+ Install BLAST+ by downloading executable from https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
The A. Gambiae PEST genome data is available to download at https://vectorbase.org/vectorbase/app/downloads/Current_Release/AgambiaePEST/fasta/data This dataset should be formatted into a BLAST database.
To build a BLAST database, use the BLAST+ 'makeblastdb' command. Detailed instructions are available on the NIH website at https://www.ncbi.nlm.nih.gov/books/NBK569841/
1 maintainer
Metadata
1 maintainer
Release files for AGambiaeHCRdesign 0.3.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| agambiaehcrdesign-0.3.0.tar.gz | 19.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| agambiaehcrdesign-0.3.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 38.9 kB
Release files / agambiaehcrdesign-0.3.0.tar.gz
| Download URL | agambiaehcrdesign-0.3.0.tar.gz |
|---|---|
| Size | 19.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
21ae31b134eae6a10ff20ee54de7934a1ecaf6d2abc93315d181b89f8812d3ca
|
|
BLAKE2b-256 checksum How to use checksums |
f3d1aae9d247f47987481e7322f55618ed09da819792eabb9dcc6802e93436c0
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.10.0
|
Release files / agambiaehcrdesign-0.3.0-py3-none-any.whl
| Download URL | agambiaehcrdesign-0.3.0-py3-none-any.whl |
|---|---|
| Size | 19.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
6786c2cd253c9175876725bca728798d4f3fcfcaf4c057b7b558089e5d0f77ba
|
|
BLAKE2b-256 checksum How to use checksums |
ebd78482345ae75fb1acb5095c5aadc512b3fdd038582bd20d0b320ba40f2342
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.10.0
|
