Update SAW V7.1.0

Documents/UserManual/ProteinPanel/ProteinPanel_128_mouse.list

@@ -0,0 +1,129 @@
+PIDIndex	PIDSequence	PIDName
+0	GCCGGACGACATTAA	Isotype_Ms_IgG1k
+1	CTCCTACCTAAACTG	Isotype_Ms_IgG2ak
+2	ATATGTATCACGCGA	Isotype_Ms_IgG2bk
+3	GATTCTTGACGACCT	Isotype_Rat_IgG2bk
+4	ATCAGATGCCCTCAT	Isotype_Rat_IgG1k
+5	GGGAGCGATTCAACT	Isotype_Rat_IgG1r
+6	AAGTCAGGTTCGTTT	Isotype_Rat_IgG2ak
+7	TCCAGGCTAGTCATT	Isotype_Rat_IgG2ck
+8	CCTGTCATTAAGACT	Isotype_Ham_IgG
+273	TTCCGAGGATGATCT	CD49f_Hu
+288	TCCTTGGATGTACCG	Integrin_b7_MsHu
+291	AACAAGACCCTTGAG	CD4_Ms
+292	GATATTCAGTGCGAC	CD102_Ms
+293	TTCATTAGCCCGCTG	CD103_Ms
+295	CGTTCCTACCTACCT	CD106_Ms
+296	AAATCTGTGCCGTAC	CD107a_Ms
+297	TTCCGTTGTTGTGAG	CD115_Ms
+299	AGAGTCTCCCTTTAG	CD11a_Ms
+300	GTTATGGACGCTTGC	CD11c_Ms
+301	GAAGCTGTATCCGAA	CD120b_Ms
+302	GTGTGAGGCACTCTT	CD127_Ms
+304	CTCACCTACCTATGG	CD134_Ms
+306	TCCCTGTATAGATGA	CD137_Ms
+307	GCGTTTGTATGTACT	CD138_Ms
+311	CAACGCCTAGAAACC	CD150_Ms
+313	TAGCTTGGGATTAAG	CD155_Ms
+314	GTGTTTGTGTTCCTG	CD159a_Ms
+316	GCGTATGTCAGTACC	CD160_Ms
+317	GAGCAAGATTAAGAC	CD163_Ms
+318	ATTGACGACAGTCAT	CD169_Ms
+319	TCAATCTCCGTCGCT	CD170_Ms
+320	GATTCCCTTGTAGCA	CD172a_Ms
+324	ACGTAGTCACCTAGT	CD185_Ms
+325	TGTCAGGTTGTATTC	CD186_Ms
+326	ATCAGCCATGTCAGT	CD19_Ms
+334	CCCTCTGGTATGGTT	CD199_Ms
+335	CAACTTGGCCGAATC	CD1d_Ms
+336	TTGCCGTGTGTTTAA	CD2_Ms
+337	TCCACTCCCTGTATA	CD20_Ms
+338	TCAATTCCGGTAGTC	CD200_Ms
+339	ATTCTTTCCCTCTGT	CD200R_Ms
+340	ATCAACTTGGAGCAG	CD200R3_Ms
+344	CATATTGGCCGTAGT	CD205_Ms
+345	GGATAATTTCGATCC	CD21_35_Ms
+347	AGGTCCTCTCTGGAT	CD22_Ms
+348	ATTCCGTCCCTAAGG	CD223_Ms
+349	ACGCAGTATTTCCGA	CD226_Ms_10E5
+351	TCTCTTGGAAGATGA	CD23_Ms
+352	TATATCTTTGCCGCA	CD24_Ms
+353	ACCATGAGACACAGT	CD25_Ms
+356	ATGGCCTGTCATAAT	CD26_Ms
+357	GATCCGTGTTGCCTA	CD270_Ms
+358	TGACCCTATTGAGAA	CD272_Ms
+360	TCGATTCCACCAACT	CD274_Ms
+362	GAAAGTCAAAGCACT	CD279_Ms
+363	GTATGTCCGCTCGAT	CD3_Ms
+364	TGTATTTACTCACCG	CD301a_Ms
+365	CCAGCTCATTCAACG	CD304_Ms
+367	GCTGTAGTATCATGT	CD31_Ms
+369	TGTGGTAGCCCTTGT	CD317_Ms
+374	GGCACTCTGTAACAT	CD357_Ms
+375	TTTGCCGCTACGACA	CD36_Ms
+377	ATTGGCACTCAGATG	CD366_Ms
+378	GCGAGAAATCTGCAT	CD371_Ms
+379	CGTATCCGTCTCCTA	CD38_Ms
+381	ATTTGTATGCTGGAG	CD40_Ms
+382	ACTTGGATGGACACT	CD41_Ms
+383	TTGGAGGGTTGTGCT	CD43_Ms
+384	TGGCTATGGAGCAGA	CD45_Ms
+386	CACCGTCATTCAACC	CD45_2_Ms
+388	AGAACCGCCGTAGTT	CD48_Ms
+389	CCATTCATTTGTGGC	CD49a_Ms
+390	CGCGTTAGTAGAGTC	CD49b_Ms
+391	CGCTTGGACGCTTAA	CD49d_Ms
+392	CAGCTCAGTGTGTTG	CD5_Ms
+393	GGAGTCAGGGTATTA	CD51_Ms
+394	ATAACCGACACAGTG	CD54_Ms
+395	ATTGTTGTCAGACCA	CD55_Ms
+396	TGGGCCTAAGTCATC	CD62L_Ms
+397	ATCCGACACGTATTA	CD63_Ms
+398	AGCAATTAACGGGAG	CD64_Ms
+399	CTTTCTTTCACGGGA	CD68_Ms
+400	TTGTATTCCGCCATT	CD69_Ms
+401	ACCGACCAGTAGACA	CD71_Ms
+402	ACACTTAACGTCTGG	CD73_Ms
+404	TAACTCAGTGCGAGT	CD79b_Ms
+406	TCTCAGGCTTCCTAG	CD83_Ms
+407	ATGTCAACTCTGGGA	CD85k_Ms
+408	CTGGATTTGTGTATC	CD86_Ms
+410	TACCCGTAATAGCGT	CD8a_Ms
+411	TTCCCTCTATGGAGC	CD8b_Ms
+412	TAGCAGTCACTCCTA	CD9_Ms
+413	CCGATCAGCCGTTTA	CD90_2_Ms
+414	GGTATTTCCTGTGGT	CD93_Ms
+415	CACAGTTGTCCGTGT	CD94_Ms
+419	CACTCTCAGTCCTAT	CX3CR1_Ms
+421	TTAACTTCAGCCCGT	F4_80_Ms
+422	AGTCACCTCGAAGCT	FceRIa_Ms
+425	GGTCACCAGTATGAT	I_A_I_E_Ms
+426	TCATATCCGTTGTCC	IgD_Ms
+429	AGCTACGCATTCAAT	IgM_Ms
+431	GCGATGGAGCATGTT	IL-33Ra_Ms
+432	GTTATGGTTCGTGTT	JAML_Ms
+433	CGATTCTTTGCGAGT	Ly108_Ms
+434	AATTCCGTCAGATGA	Ly-49A_Ms
+435	TATATCCCTCAACGC	Ly49D_Ms
+437	CCAGTAGGCTTATTA	Ly49H_Ms
+438	TTCCTTTCCTACGCA	Ly6A_E_Ms
+439	AAGTCGTGAGGCATG	Ly6C_Ms
+440	ACATTGACGCAACTA	Ly6G_Ms
+442	GTAACATTACTCGTC	NK1_1_Ms
+448	TGTAGAGTCAGACCT	PIRA_B_Ms
+450	CCGCACCTACATTAG	SiglecH_Ms
+452	TCCTATGGGACTCAG	TCR_b_Ms
+457	AACCCAAATAGCTGA	TCR_r_d_Ms
+458	GCGCGTTTGTGCTAT	TER119_Ms
+460	TGCTGGAGGGTATTC	Tim4_Ms
+462	ACATTTCCCTTGCCT	VISTA_Ms
+463	CTTGCCTTGCGATTT	CD301b_Ms
+464	TGGCTTCAGGTCCTA	CD44_MsHu
+465	CCTACACCTCATAAT	CD45R_MsHu
+466	GTAGTAGGCTAGACC	KLRG1_MsHu
+468	TGAAGGCTCATTTGT	CD11b_MsHu
+469	ACGCATTCCTTGTGT	CD29_Ms
+470	TTCTTTACCCGCCTG	CD61_Ms
+471	TTGTCACCAACTTCC	CD81_Ms
+472	TCCATTACCCACGTT	XCR1_Ms
+473	CAAGGTATGTCACTG	CD27_MsHu

Documents/UserManual/ProteinPanel/ProteinPanel_163_human.list

@@ -0,0 +1,164 @@
+PIDIndex	PIDSequence	PIDName
+13	CTACTTCCCTGTCAA	CD101_Hu
+19	CAGCCCACTGCAATA	CD107a_Hu
+20	CACTTAACTCTGGGT	CD109_Hu
+22	AACCTTCCGTCTAAG	CD112_Hu
+23	AATCACGGTCCTTGT	CD115_Hu
+24	ATGGACAGTTCGTGT	CD116_Hu
+26	TGTGTATTCCCTTGT	CD119_Hu
+27	TATATCCTTGTGAGC	CD11a_Hu
+28	TACGCCTATAACTTG	CD11c_Hu
+30	TCATTTCCTCCGATT	CD122_Hu
+31	CTTCACTCTGTCAGG	CD123_Hu
+33	GTGTGTTGTCCTATG	CD127_Hu
+34	TTTCAACGCCCTTTC	CD13_Hu
+35	CTGCATGAGACCAAA	CD131_Hu
+38	AACCCACCGTTGTTA	CD134_Hu
+40	CAGTAAGTTCGGGAC	CD137_Hu
+46	GGATAACCGCGCTTT	CD141_Hu
+47	CACTGCCGTCGATTA	CD142_Hu
+49	CCTTGGATAACATCA	CD146_Hu
+51	CTTACCTAGTCATTC	CD151_Hu
+52	ATGGTTCACGTAATC	CD152_Hu
+53	GCTAGATAGATGCAA	CD154_Hu
+54	ATCACATCGTTGCCA	CD155_Hu
+55	TATCAACCAACGCTT	CD158_Hu
+58	GGACGCTTTCCTTGA	CD158e1_Hu
+62	TACTCAGCGTGTTTG	CD169_Hu
+63	CGTGTTTAACTTGAG	CD172a_Hu
+66	TATTGGGACACTTCT	CD18_Hu
+67	AATTCAACCGTCGCC	CD185_Hu
+69	CTGGGCAATTACTCG	CD19_Hu
+71	GAGTTCCCTTACCTG	CD192_Hu
+73	AGCTTACCTGCACGA	CD194_Hu
+74	CCAAAGTAAGAGCCA	CD195_Hu
+79	GAGCTACTTCACTCG	CD1c_Hu
+81	TACGATTTGTCAGGG	CD2_Hu
+82	CACGTAGACCTTTGC	CD200_Hu
+91	AACCTAGTAGTTCGG	CD21_Hu
+92	GGGTTGTTGTCTTTG	CD22_Hu
+93	CATTTGTCTGCCGGT	CD223_Hu
+98	TCTGTATAACCGTCT	CD23_Hu
+101	AGATTCCTTCGTGTT	CD24_Hu
+102	TCGCTTGGATGGTAG	CD244_Hu
+103	TTTGTCCTGTACGCC	CD25_Hu
+106	GGTGGCTAGATAATG	CD26_Hu
+108	AGTGATGGAGCGAAC	CD267_Hu
+109	CGAAGTCGATCCGTA	CD268_Hu
+111	TGATAGAAACAGACC	CD270_Hu
+114	GTTGTCCGACAATAC	CD274_Hu
+118	ACAGCGCCGTATTTA	CD279_Hu
+120	GTATTCCCTCAGTCA	CD29_Hu
+126	GAGATGTCCGAATTT	CD303_Hu
+127	GGACTAAGTTTCGTT	CD304_Hu
+128	ATTTCCATTCCCTGT	CD305_Hu
+132	AGTATGCCATGTCTT	CD319_Hu
+133	GCTTCCGAATTACCG	CD32_Hu
+138	CTTAGCATTTCACTG	CD328_Hu
+139	TAACTCAGGGCCTAT	CD33_Hu
+140	ACAATTTGAACAGCG	CD335_Hu
+145	ACTTCCGTCGATCTT	CD35_Hu
+146	AGTTTCCACTCAGGC	CD352_Hu
+147	TAGCCGTTTCCTTTG	CD354_Hu
+149	TTCTTTGCCTTGCCA	CD36_Hu
+152	ACAGTCACTGGGCAA	CD37_Hu
+159	ACGTTGTGGCCTTGT	CD41_Hu
+160	TCCTAGTACCGAAGT	CD42b_Hu
+161	GATTAACCAGCTCAT	CD43_Hu
+162	AATCCTTCCGAATGT	CD44_Hu
+165	TCAATCCTTCCGCTT	CD45RA_Hu
+167	CTCCGAATCATGTTG	CD45RO_Hu
+168	GCATTCTGTCACCTA	CD47_Hu
+169	CTACGACGTAGAAGA	CD48_Hu
+170	ACTGATGGACTCAGA	CD49a_Hu
+171	GCTTTCTTCAGTATG	CD49b_Hu
+172	CATTAACGGGATGCC	CD5_Hu
+173	CTTTGTACGAGCAAA	CD52_Hu
+174	CTGATAGACTTGAGT	CD54_Hu
+175	GCTCATTACCCATTA	CD55_Hu
+178	AACTCCCTATGGAGG	CD57_Hu
+179	GTTCCTATGGACGAC	CD58_Hu
+180	GTCCCTGCAACTTGA	CD62L_Hu
+181	CCTTCCGTATCCCTT	CD62P_Hu
+182	GAGATGTCTGCAACT	CD63_Hu
+185	GTCTCTTGGCTTAAA	CD69_Hu
+186	TGGATTCCCGGACTT	CD7_Hu
+188	CCGTGTTCCTCATTA	CD71_Hu
+189	CAGTCGTGGTAGATA	CD72_Hu
+190	CAGTTCCTCAGTTCG	CD73_Hu
+191	ATTCTTCAACCGAAG	CD79b_Hu
+193	GTATCCTTCCTTGGC	CD81_Hu
+194	TCCCACTTCCGCTTT	CD82_Hu
+195	CCACTCATTTCCGGT	CD83_Hu
+196	CTCCCTAGTTCCTTT	CD84_Hu
+197	CCTTGTGAGGCTATG	CD85j_Hu
+199	GCCGCATGAGAAACA	CD88_Hu
+200	GAGTCACCAATCTGC	CD9_Hu
+202	GCGCTACTTCCTTGA	CD93_Hu
+203	CTTTCCGGTCCTACA	CD94_Hu
+206	ACCCGTCCCTAAGAA	CD99_Hu
+207	TGCCAGTATCACGTA	CLEC1B_Hu
+208	AGTATCGTCTCTGGG	CX3CR1_Hu
+218	CAGTCTCCGTAGAGT	IgD_Hu
+219	GGATGTACCGCGTAT	IgE_Hu
+221	TAGCGAGCCCGTATA	IgM_Hu
+222	CTTATTTCCTGCCCT	KLRG1_Hu
+227	TATAGTTCCTCTGTG	NKp80_Hu
+241	TTGCTTACCGCCAGA	TIGIT_Hu
+250	GTTATTGGACTAAGG	CD272_Hu
+252	GACAAGTGATCTGCA	CD11b_Hu
+254	GTCATTGTATGTCTG	CD150_Hu
+255	AAGTTCACTCTTTGC	CD16_Hu
+256	GTACGCAGTCCTTCT	CD161_Hu
+257	ATATGTCAGAGCACC	CD162_Hu
+258	GCTTCTCCTTCCTTA	CD163_Hu
+260	GCGATGGTAGATTAT	CD183_Hu
+262	GATCCCTTTGTCACT	CD196_Hu
+263	TTCTGGGTCCCTAGA	CD20_Hu
+265	GCACTCCTGCATGTA	CD27_Hu
+266	TGAGAACGACCCTAA	CD28_Hu
+267	ACCTTTATGCCACGG	CD31_Hu
+269	TTACCTGGTATCCGT	CD39_Hu
+271	CTCAGATGGAGTATG	CD40_Hu
+272	CCATTCAACTTCCGG	CD49d_Hu
+273	TTCCGAGGATGATCT	CD49f_Hu
+275	AGGTTGGAGTAGACT	CD61_Hu
+276	AAGTATGCCCTACGA	CD64_Hu
+277	CTGTAGCATTTCCCT	CD74_Hu
+278	GCGCAACTTGATGAT	CD8_Hu
+279	GTCTTTGTCAGTGCA	CD86_Hu
+282	CCAGCTCATTAGAGC	CD95_Hu
+287	GCCTAGTTTCCGTTT	GPR56_Hu
+122	CTCATTGTAACTCCT	CD3_Hu_UCHT1
+177	TCCTTTCCTGATAGG	CD56_Hu_5_1H11
+283	TATGCGAGGCTTATC	HLA_A_B_C_Hu
+158	TGTTCCCGCTCAACT	CD4_Hu_RPA-T4
+253	TCTCAGACCTCCGTA	CD14_Hu_M5E2
+214	AGCTACGAGCAGTAG	HLA_DR_DP_DQ_Hu
+284	AATAGCGAGCAAGTA	HLA_DR_Hu
+289	CGCGCACCCATTAAA	CD278_MsHu
+116	GTTAGTGTTAGCTTG	CD275_Hu_9F8A4
+288	TCCTTGGATGTACCG	Integrin_b7_MsHu
+240	CGTAACGTAGAGCGA	TCR_a_b_Hu
+237	TACGAGCAGTATTCA	TCR_Va7_2_Hu
+238	TCAGTCAGATGGTAT	TCR_Vd2_Hu
+210	CTCGTTTCCGTATCG	FceRIa_Hu
+95	TCTCAGTGTTTGTGG	CD226_Hu_11A8
+155	TGTACCCGCTTGTGA	CD38_Hu_HIT2
+164	TGCAATTACCCGGAT	CD45_Hu_HI30
+224	ACCCTTTACCGAATA	LOX1_Hu
+154	CATTAGAGTCTGCCA	CD371_Hu
+216	AGCTCAGCCAGTATG	Ig_light_chain_k_Hu
+217	CAGCCAGTAAGTCAC	Ig light_chain_l_Hu
+0	GCCGGACGACATTAA	Isotype_Ms_IgG1k
+1	CTCCTACCTAAACTG	Isotype_Ms_IgG2ak
+2	ATATGTATCACGCGA	Isotype_Ms_IgG2bk
+3	GATTCTTGACGACCT	Isotype_Rat_IgG2bk
+231	GGTTACTCGTTGTGT	Podoplanin_Hu
+15	GACCTCATTGTGAAT	CD103_Hu
+130	CGTGTTTGTTCCTCA	CD314_Hu
+4	ATCAGATGCCCTCAT	Isotype_Rat_IgG1k
+5	GGGAGCGATTCAACT	Isotype_Rat_IgG1r
+6	AAGTCAGGTTCGTTT	Isotype_Rat_IgG2ak
+7	TCCAGGCTAGTCATT	Isotype_Rat_IgG2ck
+8	CCTGTCATTAAGACT	Isotype_Ham_IgG

Documents/UserManual/README.md

@@ -1,19 +1,2 @@
 # Important Notifications
 This notification page is a place to record and respond the user-reported issues/bugs and inform other users who may be affected by the same bug. Meanwhile, we inform users of important improvement and version changes here. We apologize for any inconvenience that may have caused you.
-
-## SAW ST v7.0.1 (Modified Mar, 2024)
-For `mapping` module    
-1. Bug fix: fixed occasional compute crashes due to specific GTF.
-
-For `count` module
-1. Bug fix: fixed the problem in compiling dependent libraries, resulting into slow computation.
-
-For `register` module
-1. Bug fix: fixed the problem caused by manual low-angle rotating/scaling on IF image, 
-2. Bug fix: fixed occasional registration error.
-
-For `cellCut` module
-1. Bug fix: fixed the calculation error of average DNB in generated GEF.
-
-For `lasso` module
-1. Bug fix: fixed the occasional error of discrepancy between targeted lasso region and GEF.