224 Commits

Author	SHA1	Message	Date
Adri K. Grow	f5ca94b51c	Update ReadMapping.py	2025-08-27 13:18:28 -04:00
Adri K. Grow	0fc18547d6	Update ReadMapping.py	2025-08-22 13:16:37 -04:00
Adri K. Grow	fee7125729	Update ProcessAndRenameAssembledData.py	2025-08-21 10:40:08 -04:00
Adri K. Grow	c92cfb1b19	Update ReadMapping.py ... Making things more universally applicable rather than keeping the hardcoded index range	2025-08-18 14:13:11 -04:00
Adri K. Grow	5fcd3b937e	Update CladeGrabbing.py	2025-08-18 10:56:17 -04:00
Adri K. Grow	20d3926f10	Update CladeGrabbing.py ... Adding new optional arguments to support two-step clade filtering within one run of the script.	2025-08-18 10:54:25 -04:00
Adri K. Grow	586a9e0c63	Update CladeGrabbing.py	2025-07-08 07:54:58 -04:00
Katzlab	aec7f6caf9	Update ColorByClade.py ... Changed to root on bacteria (Ba) and not prokaryotes (Ba, Za).... did not test	2025-07-01 16:18:54 -04:00
Godwin N. Ani	5486c4289b	Add files via upload	2025-07-01 11:11:21 -04:00
Adri K. Grow	0b1feed651	Update ProcessAndRenameAssembledData.py	2025-06-27 12:39:05 -04:00
Adri K. Grow	d33ac6c2c3	Update Trim_Reads.py	2025-06-26 15:55:15 -04:00
Adri K. Grow	c767bd9a0a	Update Trim_Reads.py	2025-06-16 11:25:08 -04:00
Adri K. Grow	c84f3387ff	Update Trim_Reads.py	2025-06-13 12:41:35 -04:00
Adri K. Grow	3e4f4987a2	Update Trim_Reads.py	2025-06-13 12:41:17 -04:00
Katzlab	e7facbf6e7	Update PlotComps.r ... Fixed typo by changing geom_line(data = enc_null, aes(GC3, ENc)) to geom_line(data = enc_null, aes(GC3S, ENc))	2025-06-12 04:27:20 -04:00
Katzlab	3fe4ee3ae5	Update CUB.py ... Updates to notes only, including clarifying that we use GC3 and GC3S interchangeably .. though GC3S probably most correct	2025-06-12 04:25:47 -04:00
GiuliaRibeiro	fdf525d433	Add files via upload	2025-06-11 10:17:50 -04:00
Adri K. Grow	4da74765ee	Add files via upload	2025-04-06 23:36:01 -04:00
Adri K. Grow	6a9ae23e8c	Delete Utilities/for_fastas/Cluster.py	2025-04-06 23:35:47 -04:00
Godwin N. Ani	d7577022c4	Update CladeSizes.py	2025-03-24 15:01:48 -04:00
Godwin N. Ani	9b6b28ac03	Update Cluster.py	2025-03-21 13:48:23 -04:00
Godwin N. Ani	31cb84fa28	Update Cluster.py	2025-03-21 13:45:49 -04:00
Godwin N. Ani	a2ec0edb37	Update Cluster.py	2025-03-21 13:43:08 -04:00
Godwin N. Ani	3d8cd2e221	Update Cluster.py	2025-03-21 13:42:57 -04:00
Godwin Ani	e18b3dfe0c	Update Cluster.py	2025-03-21 13:22:21 -04:00
Adri K. Grow	1aebef4725	Delete Utilities/For_Assemblies/ProcessAndRenamePlateTranscripts.py	2025-02-13 16:30:03 -05:00
Adri K. Grow	dfd826ee94	Add files via upload	2025-02-13 16:29:13 -05:00
Godwin Ani	45de3036c9	Update ShortenTips.py	2025-02-04 18:59:31 -05:00
Godwin Ani	7e9b90c79b	Shorten tree tip names	2025-02-04 18:58:53 -05:00
Adri K. Grow	fe7ef7b71a	Update and rename ProcessAndRenamePlateTranscripts_AKG.py to ProcessAndRenamePlateTranscripts.py	2025-01-15 11:25:16 -05:00
Adri K. Grow	2ad02897c8	Add files via upload	2025-01-15 11:22:39 -05:00
Auden Cote-L'Heureux	1e543b3989	Adding TPM calculating script (Salmon)	2025-01-09 12:06:10 -05:00
Auden Cote-L'Heureux	a8a2a5ff2d	Moving CountTaxonOccurence.py	2025-01-08 10:38:23 -05:00
Adri K. Grow	1c309f8e10	Update ReadMapping.py	2024-12-06 12:20:50 -05:00
Adri K. Grow	a0b45ed2c8	Update CladeSizes.py ... Modified to work with clade grabbed input file names.	2024-11-11 08:59:47 -05:00
Auden Cote-L'Heureux	fb6e7aa6e7	Changing CladeGrabbing.py to use less than or equal to for number of contaminants	2024-11-01 10:34:57 -04:00
Auden Cote-L'Heureux	d249add545	Add files via upload	2024-10-17 16:45:55 -04:00
Katzlab	4676ef2b53	Delete Utilities/README.md	2024-08-14 11:59:56 -04:00
Katzlab	dbbef111b5	Delete Utilities/for_MSAs/README.md	2024-08-09 10:05:27 -04:00
Katzlab	6112f3ebc4	Delete Utilities/for_fastas/README.md	2024-08-09 10:05:19 -04:00
Katzlab	e2298810d2	Delete Utilities/for_trees/README.md	2024-08-09 10:04:55 -04:00
Adri K. Grow	b667dd6478	Update CountTaxonOccurence.py ... updated header	2024-08-07 18:16:01 -04:00
Godwin Ani	d240be1877	Update CUB.py	2024-07-19 12:53:21 -04:00
Katzlab	20e38f57b5	Update ColorByClade.py ... added example use and note on how to turn off rooting	2024-07-16 09:23:57 -04:00
Katzlab	6a86fded41	Update CountTaxonOccurence.py ... improving header	2024-06-09 13:02:38 -04:00
Katzlab	7aac410d85	Update CountTaxonOccurence.py ... adding option to look at only focal major clades	2024-06-09 13:01:59 -04:00
Katzlab	552e958952	Update CountTaxonOccurence.py ... updated to include summary of major and minor clades, and to allow target minor clade list	2024-06-09 12:44:26 -04:00
Katzlab	436cad7238	Purple color for EE	2024-06-06 17:23:26 -04:00
Godwin Ani	fd7b2e7302	rooting	2024-06-04 12:47:49 -04:00
Godwin Ani	405217e2a2	Update Gappiness.py	2024-06-03 16:09:29 -04:00