J vdj
Author: s | 2025-04-24
Describes the data type of the samplerna, vdj, adt, or crispr. rna refers to gene expression data (cellranger count), vdj refers to V(D)J data (cellranger vdj), adt refers to VDJ Recombinases / physiology Substances DNA-Binding Proteins Nuclear Proteins RAG2 protein, human V(D)J recombination activating protein 2 VDJ Recombinases
The VDJ recombination process, in which individual V, D, and J
Or a custom model folder can be indicated.OptionsDescription--humanTRADefault human T cell alpha chain model (VJ)--humanTRBDefault human T cell beta chain model (VDJ)--mouseTRBDefault mouse T cell beta chain model (VDJ)--humanIGHDefault human B cell heavy chain model (VDJ)--set_custom_model_VJ PATH/TO/MODEL_FOLDER/Specifies the directory PATH/TO/MODEL_FOLDER/ of a custom VJ generative model--set_custom_model_VDJ PATH/TO/MODEL_FOLDER/Specifies the directory PATH/TO/MODEL_FOLDER/ of a custom VDJ generative modelNote, if specifying a folder for a custom VJ recombination model(e.g. an alpha or light chain model) or a custom VDJ recombination model(e.g. a beta or heavy chain model), the folder must contain the following fileswith the exact naming convention:model_params.txt (IGoR inference param file)model_marginals.txt (IGoR inference marginal file)V_gene_CDR3_anchors.csv (V anchor residue position and functionality file)J_gene_CDR3_anchors.csv (J anchor residue position and functionality file)The console scripts can only read files of the assumed anchor.csv/IGoR syntaxes. If the advanced user wants to read in models from files of other formats please read the discussion in the Python module section and the documentation of load_model.py.compute_pgen.py (olga-compute_pgen)This script will compute the generation probabilities (pgens) of sequences, as defined by a specified generative model. The sequences must be TRIMMED TO ONLY THE CDR3 region as defined by the V and J anchor files (default is to INCLUDE the conserved residues of the C in the V region and the F/W in the J region).Each sequence will be determined to be one of:'Amino acid' sequence including any ambiguous amino acid symbols (seeOptions for alphabet_file to specify custom symbols)Nucleotide sequence (in-frame)Regular expression template for 'amino acid sequences'This script can read in sequences and output pgens in one of three modes (determined automatically based on the input arguments):Pass CDR3 sequences as arguments, output is printed to stdout.Read in CDR3 sequences from a file, output is printed to stdout.Read in CDR3 sequences from a file, output to a file, dynamic display with time updates printed to stdout.Full options can be printed by: $ olga-compute_pgen -hMode 1):This mode is provided as a way to quickly compute pgen of just a single or couple of sequences. It is not advisable to use this method to set up a loop over a lot of sequences as each call Describes the data type of the samplerna, vdj, adt, or crispr. rna refers to gene expression data (cellranger count), vdj refers to V(D)J data (cellranger vdj), adt refers to VDJ Recombinases / physiology Substances DNA-Binding Proteins Nuclear Proteins RAG2 protein, human V(D)J recombination activating protein 2 VDJ Recombinases For the input! Well it looks like this might not really be what I'm looking for then. I'm looking to use Virtual DJ to cue up music and play it, and a mixer to be able to cross-fade between tracks, with an input for my iPad in case my computer or my Virtual DJ crashes. Any ideas on hardware options? Also not sure how much this matters but I have Mac Yosemite and currently using the LE versions of VDJ 7 and 8 (although 8 won't recognize my iTunes playlists, grr). Thanks all! Posted Thu 05 Mar 15 @ 6:27 pm djjohnnyroxPRO InfinityMember since 2010 One of the controllers I ise is Hercules mk4. I can use vdj and aux input at the same time. Settings in the Hercules Dj console are:Line insHeadphone AsioWhen set this way I click on vdj aux in and it uses the sound from my line input. The rmx2 may or may not be different J Posted Thu 05 Mar 15 @ 6:31 pm djdadPRO InfinityDevelopment ManagerMember since 2005 Your controller is capable of doing that, but LineIns need to be added in the Audio Setup of VirtualDJ in order the AUX Inputs to go though VirtualDJ as LineIns.Not sure if the VirtualDJ LE7 can do that, but certainly both Pro ver 7 and Pro Infinity ver 8 can do.Which version/product of VirtualDJ are you currently using ? Posted Fri 06 Mar 15 @ 3:30 am reenasamaanLE userMember since 2015 With Virtual DJ 8 (theComments
Or a custom model folder can be indicated.OptionsDescription--humanTRADefault human T cell alpha chain model (VJ)--humanTRBDefault human T cell beta chain model (VDJ)--mouseTRBDefault mouse T cell beta chain model (VDJ)--humanIGHDefault human B cell heavy chain model (VDJ)--set_custom_model_VJ PATH/TO/MODEL_FOLDER/Specifies the directory PATH/TO/MODEL_FOLDER/ of a custom VJ generative model--set_custom_model_VDJ PATH/TO/MODEL_FOLDER/Specifies the directory PATH/TO/MODEL_FOLDER/ of a custom VDJ generative modelNote, if specifying a folder for a custom VJ recombination model(e.g. an alpha or light chain model) or a custom VDJ recombination model(e.g. a beta or heavy chain model), the folder must contain the following fileswith the exact naming convention:model_params.txt (IGoR inference param file)model_marginals.txt (IGoR inference marginal file)V_gene_CDR3_anchors.csv (V anchor residue position and functionality file)J_gene_CDR3_anchors.csv (J anchor residue position and functionality file)The console scripts can only read files of the assumed anchor.csv/IGoR syntaxes. If the advanced user wants to read in models from files of other formats please read the discussion in the Python module section and the documentation of load_model.py.compute_pgen.py (olga-compute_pgen)This script will compute the generation probabilities (pgens) of sequences, as defined by a specified generative model. The sequences must be TRIMMED TO ONLY THE CDR3 region as defined by the V and J anchor files (default is to INCLUDE the conserved residues of the C in the V region and the F/W in the J region).Each sequence will be determined to be one of:'Amino acid' sequence including any ambiguous amino acid symbols (seeOptions for alphabet_file to specify custom symbols)Nucleotide sequence (in-frame)Regular expression template for 'amino acid sequences'This script can read in sequences and output pgens in one of three modes (determined automatically based on the input arguments):Pass CDR3 sequences as arguments, output is printed to stdout.Read in CDR3 sequences from a file, output is printed to stdout.Read in CDR3 sequences from a file, output to a file, dynamic display with time updates printed to stdout.Full options can be printed by: $ olga-compute_pgen -hMode 1):This mode is provided as a way to quickly compute pgen of just a single or couple of sequences. It is not advisable to use this method to set up a loop over a lot of sequences as each call
2025-04-21For the input! Well it looks like this might not really be what I'm looking for then. I'm looking to use Virtual DJ to cue up music and play it, and a mixer to be able to cross-fade between tracks, with an input for my iPad in case my computer or my Virtual DJ crashes. Any ideas on hardware options? Also not sure how much this matters but I have Mac Yosemite and currently using the LE versions of VDJ 7 and 8 (although 8 won't recognize my iTunes playlists, grr). Thanks all! Posted Thu 05 Mar 15 @ 6:27 pm djjohnnyroxPRO InfinityMember since 2010 One of the controllers I ise is Hercules mk4. I can use vdj and aux input at the same time. Settings in the Hercules Dj console are:Line insHeadphone AsioWhen set this way I click on vdj aux in and it uses the sound from my line input. The rmx2 may or may not be different J Posted Thu 05 Mar 15 @ 6:31 pm djdadPRO InfinityDevelopment ManagerMember since 2005 Your controller is capable of doing that, but LineIns need to be added in the Audio Setup of VirtualDJ in order the AUX Inputs to go though VirtualDJ as LineIns.Not sure if the VirtualDJ LE7 can do that, but certainly both Pro ver 7 and Pro Infinity ver 8 can do.Which version/product of VirtualDJ are you currently using ? Posted Fri 06 Mar 15 @ 3:30 am reenasamaanLE userMember since 2015 With Virtual DJ 8 (the
2025-04-17COMMENT_DELIMITERcharacter or string to indicate comment or header lines to skip.generate_sequences.py (olga-generate_sequences)This program will generate a file of Monte Carlo sampling from a specified generative V(D)J model. The sequences generated will have NO ERRORS.It is required to specify the number of sequences to be generated. This is done with -n (see Options).If a file is specified to write to (using -o, see Options), the generated sequences are written to the file, otherwise they are printed to stdout.The default is to record both the nucleotide CDR3 sequence and the amino acid CDR3 sequence. This can be specified (see Options).The V/J genes used to generate each sequence can be recorded or not. Default is to record them, but this can be toggled off with --record_genes_off (see Options).Full options can be printed by: $ olga-generate_sequences -hExample calls:Print 20 generated sequences to stdout$ olga-generate_sequences --humanTRB -n 20Write 200 generated sequences to example_seqs.tsv$ olga-generate_sequences --humanTRB -o example_seqs.tsv -n 200Write 20,000 generated sequences to example_seqs.tsv$ olga-generate_sequences --humanTRB -o example_seqs.tsv -n 2e4Write only the amino acid sequences$ olga-generate_sequences --humanTRB -o example_seqs.tsv -n 200 --seq_type amino_acidSelected OptionsDescription-h, --helpshow full Options list and exit-o PATH/TO/FILEwrite CDR3 sequences to PATH/TO/FILE-n Nspecify the number of sequences to generate.--seed SEEDset seed for pseudorandom number generator. Default is to not set a seed.--seq_type SEQ_TYPEdeclare sequence type for output sequences. Choices: 'all' [default], 'ntseq', 'aaseq'--time_updates_offturn time updates off.--record_genes_offturn off recording V and J gene info.-d DELIMITERdeclare delimiter choice. Default is tab for .tsv output files, comma for .csv files, and tab for all others. Choices: 'tab', 'space', ',', ';', ':'--raw_delimiter DELIMITERdeclare delimiter choice as a raw string.Using the OLGA modules in a Python script (advanced users)In order to incorporate the core algorithm into an analysis pipeline (or to write your own script wrappers) all that is needed is to import the modules and load up a generative model. Each module defines some classes that only a few methods get called on.As the generative model structure is different between VDJ recombination and VJ recombination the algorithms to compute Pgen for the two are different. For this reason, different objects are defined for VDJ recombination models
2025-04-20From yellow to bluegrey Posted Wed 02 Nov 22 @ 10:04 pm J J ZrnPRO InfinityMember since 2019 Denny DennYo wrote :Version History 3.3.4b - 2022/11/02 Bugfix - Position correctures 4 BTN PADs change - Master Color from yellow to bluegrey This is fantastic!. When does it go live?..or put in the extensions so we can get it?Thanks again! Posted Fri 04 Nov 22 @ 3:46 pm DennYo BeatsPRO InfinityModeratorMember since 2010 Supporters get the Update direct after upload here. I send these per Mail.Here comes the update after check the Skin by Atomix-VirtualDJ. Posted Fri 04 Nov 22 @ 6:01 pm J J ZrnPRO InfinityMember since 2019 Denny DennYo wrote :Supporters get the Update direct after upload here. I send these per Mail.Here comes the update after check the Skin by Atomix-VirtualDJ.ohhh..okay..thanks! Posted Sat 05 Nov 22 @ 1:20 am Dj ChachiPRO InfinityMember since 2006 Just wanted to Thank You Denn Yo, for your hard work and creativity. This is the only skin that made me switch from the Default VDJ Skin to a Custom.Definitely your custom skin is off charts a Home Run, I'm loving it.Thank You Posted Sun 06 Nov 22 @ 1:40 pm DennYo BeatsPRO InfinityModeratorMember since 2010 Version 3.3.4b is online Posted Mon 07 Nov 22 @ 1:33 pm J J ZrnPRO InfinityMember since 2019 Could you please tell me the location of the font sizes on the text document for the cue points? Or at least the fontsize and i can search by that.
2025-03-27