Difference between revisions of "Resources"
From Zhang Laboratory
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We are committed to making resources generated in the lab, including datasets and software tools, available for the research communities. | We are committed to making resources generated in the lab, including datasets and software tools, available for the research communities. | ||
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==Software== | ==Software== | ||
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| − | *'''CTK''': CLIP Tool Kit, previously known as CIMS ([[CTK_Documentation|documentation]], [[CTK_Documentation#Download|download]], [ | + | *'''CTK''': CLIP Tool Kit, previously known as CIMS ([[CTK_Documentation|documentation]], [[CTK_Documentation#Download|download]], [http://groups.google.com/forum/#!forum/ctk-user-group user group]) |
| + | *'''DeltaSplice''': deep neural network based prediction of alternative splicing and splicing-altering mutations from pre-mRNA sequences ([http://github.com/chaolinzhanglab/DeltaSplice site]) | ||
*'''mCarts''': hidden Markov model (HMM) based methods to predict clusters RNA motif sites ([[mCarts_Documentation|documentation]], [[mCarts_Documentation#Download|download]]) | *'''mCarts''': hidden Markov model (HMM) based methods to predict clusters RNA motif sites ([[mCarts_Documentation|documentation]], [[mCarts_Documentation#Download|download]]) | ||
*'''mCross''': modeling RBP binding specificity by registering protein-RNA crosslink sites ([[MCross|site]]) | *'''mCross''': modeling RBP binding specificity by registering protein-RNA crosslink sites ([[MCross|site]]) | ||
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*'''NDDcluster''': nonparametric "shape free" clustering algorithm based on normalized density derivatives ([[NDDcluster|site]]) | *'''NDDcluster''': nonparametric "shape free" clustering algorithm based on normalized density derivatives ([[NDDcluster|site]]) | ||
*'''OLego''': A tool for fast and accurate mapping of exon-junction reads ([[OLego|site]], [[OLego_Documentation|documentation]], [[OLego_Documentation#Download|download]]) | *'''OLego''': A tool for fast and accurate mapping of exon-junction reads ([[OLego|site]], [[OLego_Documentation|documentation]], [[OLego_Documentation#Download|download]]) | ||
| + | *'''PxR3D-map''': structure-based prediction of protein-RNA photocrosslink sites ([http://github.com/chaolinzhanglab/PxR3D site]) | ||
*'''Splicescope''': prediction of neuronal maturation stages using splicing profile ([[Splicescope|site]]) | *'''Splicescope''': prediction of neuronal maturation stages using splicing profile ([[Splicescope|site]]) | ||
*'''Quantas''': A pipeline to analyze alternative splicing using RNA-Seq ([[Quantas_Documentation|documentation]],[[Quantas_Documentation#Download|download]]) | *'''Quantas''': A pipeline to analyze alternative splicing using RNA-Seq ([[Quantas_Documentation|documentation]],[[Quantas_Documentation#Download|download]]) | ||
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*[[Cortex AS]]: Cortex_AS|A database of known and novel AS events in the brain | *[[Cortex AS]]: Cortex_AS|A database of known and novel AS events in the brain | ||
*[[Autism_D-score|Autism D-score]]: Prioritization of autism risk genes using D-score derived from CSN cell type-specific gene expression. | *[[Autism_D-score|Autism D-score]]: Prioritization of autism risk genes using D-score derived from CSN cell type-specific gene expression. | ||
| + | *[http://zhanglab.c2b2.columbia.edu/data/mCross/eCLIP_mCross_PWM.tgz mCross RBP motifs]: PWMs of 112 RBPs from our mCross paper, also see the [http://zhanglab.c2b2.columbia.edu/mCrossBase/ web interface] | ||
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| + | ==Reagents== | ||
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| + | [[File:Experiments.jpg|120px|center|link=]] | ||
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| + | *Plasmids: [http://www.addgene.org/Chaolin_Zhang/ available at Addgene] | ||
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Latest revision as of 09:02, 30 May 2024
 We are committed to making resources generated in the lab, including datasets and software tools, available for the research communities. |
Software
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Datasets
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Reagents
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