212 Commits

Author	SHA1	Message	Date
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
Godwin Ani	35376a279c	Update Cluster.py	2024-06-03 16:08:46 -04:00
Godwin Ani	f0799852b8	Update and rename RenameTips_v1.0.py to RenameTips.py	2024-06-03 16:07:31 -04:00
Godwin Ani	2635deefc1	Update and rename CountTaxonOccurence_v2.0.py to CountTaxonOccurence.py	2024-06-03 16:07:05 -04:00
Godwin Ani	81e5d5655e	Update and rename ContaminationBySisters_v2.2.py to ContaminationBySisters.py	2024-06-03 16:06:42 -04:00
Godwin Ani	a9ea2881be	Update and rename ColorByClade_v2.2.py to ColorByClade.py	2024-06-03 16:06:19 -04:00
Godwin Ani	6a9c37b71f	Update and rename CladeSizes_v2.0.py to CladeSizes.py	2024-06-03 16:06:00 -04:00
Godwin Ani	577e95d5e9	fix copying files twice	2024-06-03 16:05:35 -04:00
Godwin Ani	2a55025595	Delete Utilities/for_trees/ColorByClade_v3.2.py	2024-06-03 16:04:59 -04:00
Godwin Ani	c41de01a2c	Update and rename CladeGrabbing_v3.2.py to CladeGrabbing.py	2024-06-03 16:03:51 -04:00
Godwin Ani	160c4e58cc	Fix copying the files twice	2024-06-03 16:03:13 -04:00
Godwin Ani	19e19c7403	Update and rename ReadMapping_v2.0.py to ReadMapping.py	2024-06-03 16:00:49 -04:00
Godwin Ani	ac36890622	Update and rename QuerySRA_v1.0.py to QuerySRA.py	2024-06-03 16:00:31 -04:00