RNA-seq~clustering

Clustering with Pearson correlation

input_1:Expression table (e.g. FPKM, RPM, TPM) with gene name (row) and sample name (column)

input_1/isoforms.count_table

transcript_id	dark_hungry	light_hungry	dark_full_1	light_full_1	dark_full_2	dark_full_3	light_full_2	light_full_3
TRINITY_DN7563_c0_g2_i3	13725.6	12951.2	15533.4	7579.31	11466.2	5429.06	7049.13	8793.38
TRINITY_DN9390_c0_g2_i1	10927	11019	10390	8506	6474	11330	12592	9826
TRINITY_DN58785_c0_g1_i1	6822.84	4586.73	7651.93	2137.14	2694.56	2684.63	5056.06	5386
TRINITY_DN2540_c0_g2_i1	169.702	16.136	3618.25	390.223	1119.21	4083.87	8456.81	11.7695
TRINITY_DN157626_c0_g1_i2	2303	2068.44	9544.42	9535.6	9766.3	7373.62	324.01	12194.1
TRINITY_DN1411_c0_g1_i8	0	42.6395	1903.21	35.6451	503.036	1387.73	769.922	954.528
TRINITY_DN17_c0_g1_i1	30450.2	22894.8	17855.8	19412.1	63130.7	169754	168824	114037
TRINITY_DN10138_c0_g1_i6	0	1775.71	3469.18	3656.52	5077.84	7454.87	8988.5	5966.85
TRINITY_DN4268_c0_g3_i2	60716	62467	73600	83959	111352	177154	257583	128860

Option

input_1/isoforms.count_table

Output

output.table.txt

id	dark_hungry	light_hungry	dark_full_1	light_full_1	dark_full_2	dark_full_3	light_full_2	light_full_3	cluster
TRINITY_DN4268_c0_g3_i2	15.8898128891427	15.9308297203017	16.1674377475334	16.3574145461795	16.7647809012362	17.4346526589075	17.9746834567187	16.9754561700984	1
TRINITY_DN17_c0_g1_i1	14.8942114615378	14.4827953545137	14.1241859472559	14.2447428941761	15.9460769798274	17.3730945429803	17.36516903195	16.7991551170419	1
TRINITY_DN2151_c0_g1_i2	15.3597426981721	15.7334390828994	16.5162294190684	15.7543838694481	15.5999622248304	16.3263627721701	16.7886163862508	16.1645828965482	2
TRINITY_DN2745_c0_g1_i3	14.6146178325688	13.9268241202094	13.4917904779985	14.0391846703067	15.7030113436099	16.5428157503405	16.7000739043565	17.0858562360519	3
TRINITY_DN12_c0_g1_i5	13.9866242517522	11.604094495882	14.8828722729475	13.7565146255331	14.4721640730987	15.7774351270858	17.4632369806393	6.19161989310194	4
TRINITY_DN476_c0_g1_i5	13.3387503081345	8.98099065946779	13.5846337241571	13.6614552363688	12.9961344897207	13.4889698363927	17.2161585072128	6.80745796802321	4
TRINITY_DN6885_c0_g1_i1	14.1088674481119	13.9713459601729	13.0827328553609	13.533852882101	14.6033713474287	15.4229582873663	15.3353031147884	15.3271105053864	3
TRINITY_DN13751_c0_g1_i1	13.6495930065879	13.0007042690112	13.095561855131	13.4283601727043	14.8004449425638	15.4264285688754	15.4914773455681	15.3912100192528	1
TRINITY_DN3_c0_g1_i3	13.1168475168862	10.0348539737321	13.8141618521845	13.0686607351934	13.7932375092361	14.6196296572064	16.9449750855334	6.40694816870921	4

cluster.1.png

cluster.2.png

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