taking fully advantage of our algorithm might involve coordination between multiple colleagues in a lab who are constructing plasmids with different expected sequences.
This is something a local core like GCEC can help with
10,000 Matching Annotations
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it could be further reduced by executing time-consuming dynamic programming only for some query-reference pairs that necessitate high levels of accuracy and by introducing parallel computing
Nice, Any other ideas to reduce RAM use?
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theoretical minimum number of reads that is required for the reliable consensus calculation is 30 reads per plasmid
Does this depend on the plasmid length and the preperation kit before sequencing that determines fragmentation?
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sc-5275, Santa Cruz Biotechnology
DOI: 10.7554/eLife.92796.2
Resource: (Santa Cruz Biotechnology Cat# sc-5275, RRID:AB_627877)
Curator: @areedewitt04
SciCrunch record: RRID:AB_627877
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926-68021, Li-COR Biosciences
DOI: 10.7554/eLife.92796.2
Resource: (LI-COR Biosciences Cat# 926-68021, RRID:AB_10706309)
Curator: @areedewitt04
SciCrunch record: RRID:AB_10706309
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sc-376818, Santa Cruz Biotechnology
DOI: 10.7554/eLife.92796.2
Resource: (Santa Cruz Biotechnology Cat# sc-376818, RRID:AB_2797313)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2797313
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ab30871, Abcam
DOI: 10.7554/eLife.92796.2
Resource: (Abcam Cat# ab30871, RRID:AB_2208084)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2208084
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ab41927, Abcam
DOI: 10.7554/eLife.92796.2
Resource: (Abcam Cat# ab41927, RRID:AB_941621)
Curator: @areedewitt04
SciCrunch record: RRID:AB_941621
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elifesciences.org elifesciences.org
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Jellyfish
DOI: 10.7554/eLife.92618.2
Resource: Jellyfish (RRID:SCR_005491)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_005491
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elifesciences.org elifesciences.org
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Jackson Labs, 007914
DOI: 10.7554/eLife.90596.2
Resource: (IMSR Cat# JAX_007914,RRID:IMSR_JAX:007914)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:007914
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Jackson Labs, 028364
DOI: 10.7554/eLife.90596.2
Resource: RRID:IMSR_JAX:028364
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:028364
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mouse genomic BAC library
DOI: 10.7554/eLife.90596.2
Resource: Gene Expression Nervous System Atlas (RRID:SCR_002721)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_002721
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Jackson Labs, 027720
DOI: 10.7554/eLife.90596.2
Resource: (IMSR Cat# JAX_027720,RRID:IMSR_JAX:027720)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:027720
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Jackson labs, 021504
DOI: 10.7554/eLife.90596.2
Resource: (IMSR Cat# JAX_021504,RRID:IMSR_JAX:021504)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:021504
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Jackson Labs, 007900
DOI: 10.7554/eLife.90596.2
Resource: (IMSR Cat# JAX_007900,RRID:IMSR_JAX:007900)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:007900
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Jackson Labs, 026220
DOI: 10.7554/eLife.90596.2
Resource: (IMSR Cat# JAX_026220,RRID:IMSR_JAX:026220)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:026220
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Jackson Labs, 027719
DOI: 10.7554/eLife.90596.2
Resource: (IMSR Cat# JAX_027719,RRID:IMSR_JAX:027719)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:027719
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elifesciences.org elifesciences.org
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Stan
DOI: 10.7554/eLife.89892.2
Resource: Stan (RRID:SCR_018459)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_018459
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elifesciences.org elifesciences.org
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BEAST
DOI: 10.7554/eLife.87018.4
Resource: BEAST (RRID:SCR_010228)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_010228
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elifesciences.org elifesciences.org
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Addgene: 74099
DOI: 10.7554/eLife.107067.1
Resource: RRID:Addgene_74099
Curator: @evieth
SciCrunch record: RRID:Addgene_74099
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HEK293S GnTI- (CRL-3022)
DOI: 10.7554/eLife.107067.1
Resource: (RRID:CVCL_A785)
Curator: @evieth
SciCrunch record: RRID:CVCL_A785
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HEK293 (CRL-1573)
DOI: 10.7554/eLife.107067.1
Resource: (DSMZ Cat# ACC-305, RRID:CVCL_0045)
Curator: @evieth
SciCrunch record: RRID:CVCL_0045
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elifesciences.org elifesciences.org
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#36355 GD VDRC
DOI: 10.7554/eLife.106169.1
Resource: RRID:Flybase_FBst0461646
Curator: @evieth
SciCrunch record: RRID:Flybase_FBst0461646
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#26899 Bloomington Drosophila Stock Center
DOI: 10.7554/eLife.106169.1
Resource: RRID:BDSC_26899
Curator: @evieth
SciCrunch record: RRID:BDSC_26899
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#5073 Bloomington Drosophila Stock Center
DOI: 10.7554/eLife.106169.1
Resource: RRID:BDSC_5073
Curator: @evieth
SciCrunch record: RRID:BDSC_5073
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#6000 VDRC
DOI: 10.7554/eLife.106169.1
Resource: RRID:Flybase_FBst0451785
Curator: @evieth
SciCrunch record: RRID:Flybase_FBst0451785
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#35787 Bloomington Drosophila Stock Center
DOI: 10.7554/eLife.106169.1
Resource: RRID:BDSC_35787
Curator: @evieth
SciCrunch record: RRID:BDSC_35787
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elifesciences.org elifesciences.org
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Bloomington Stock #41347
DOI: 10.7554/eLife.106148.1
Resource: RRID:BDSC_41347
Curator: @evieth
SciCrunch record: RRID:BDSC_41347
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Bloomington Stock Center #8848
DOI: 10.7554/eLife.106148.1
Resource: RRID:BDSC_8848
Curator: @evieth
SciCrunch record: RRID:BDSC_8848
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Bloomington Stock Center #1495
DOI: 10.7554/eLife.106148.1
Resource: RRID:BDSC_1495
Curator: @evieth
SciCrunch record: RRID:BDSC_1495
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Bloomington Stock Center #55134
DOI: 10.7554/eLife.106148.1
Resource: RRID:BDSC_55134
Curator: @evieth
SciCrunch record: RRID:BDSC_55134
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Bloomington Stock #25796
DOI: 10.7554/eLife.106148.1
Resource: RRID:BDSC_25796
Curator: @evieth
SciCrunch record: RRID:BDSC_25796
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Bloomington Stock Center #58374
DOI: 10.7554/eLife.106148.1
Resource: RRID:BDSC_58374
Curator: @evieth
SciCrunch record: RRID:BDSC_58374
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elifesciences.org elifesciences.org
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Jackson Laboratory, stock #000664
DOI: 10.7554/eLife.105774.1
Resource: RRID:IMSR_JAX:000664
Curator: @evieth
SciCrunch record: RRID:IMSR_JAX:000664
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elifesciences.org elifesciences.org
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ABCD
DOI: 10.7554/eLife.105537.1
Resource: ABCD Study (RRID:SCR_015769)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_015769
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FreeSurfer
DOI: 10.7554/eLife.105537.1
Resource: FreeSurfer (RRID:SCR_001847)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_001847
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elifesciences.org elifesciences.org
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d
DOI: 10.7554/eLife.105339.1
Resource: (Abcam Cat# ab5131, RRID:AB_449369)
Curator: @areedewitt04
SciCrunch record: RRID:AB_449369
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b
DOI: 10.7554/eLife.105339.1
Resource: (Active Motif Cat# 39664, RRID:AB_2615006)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2615006
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Math1>Cre
DOI: 10.7554/eLife.105339.1
Resource: RRID:IMSR_JAX:011104
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:011104
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Ptch1+/-
DOI: 10.7554/eLife.105339.1
Resource: (IMSR Cat# JAX_003081,RRID:IMSR_JAX:003081)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:003081
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i
DOI: 10.7554/eLife.105339.1
Resource: (Abcam Cat# ab4729, RRID:AB_2118291)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2118291
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Math1>GFP
DOI: 10.7554/eLife.105339.1
Resource: None
Curator: @areedewitt04
SciCrunch record: RRID:MGI:4456122
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t
DOI: 10.7554/eLife.105339.1
Resource: (Millipore Cat# 07-449, RRID:AB_310624)
Curator: @areedewitt04
SciCrunch record: RRID:AB_310624
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i
DOI: 10.7554/eLife.105339.1
Resource: (Active Motif Cat# 39097, RRID:AB_2732926)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2732926
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n
DOI: 10.7554/eLife.105339.1
Resource: (Abcam Cat# ab8895, RRID:AB_306847)
Curator: @areedewitt04
SciCrunch record: RRID:AB_306847
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A
DOI: 10.7554/eLife.105339.1
Resource: (Abcam Cat# ab8580, RRID:AB_306649)
Curator: @areedewitt04
SciCrunch record: RRID:AB_306649
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o
DOI: 10.7554/eLife.105339.1
Resource: (Abcam Cat# ab9050, RRID:AB_306966)
Curator: @areedewitt04
SciCrunch record: RRID:AB_306966
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elifesciences.org elifesciences.org
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Open Ephys
DOI: 10.7554/eLife.105088.1
Resource: Open Ephys (RRID:SCR_021624)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_021624
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SLEAP
DOI: 10.7554/eLife.105088.1
Resource: Social LEAP (RRID:SCR_021382)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_021382
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elifesciences.org elifesciences.org
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MATLAB
DOI: 10.7554/eLife.103959.1
Resource: MATLAB (RRID:SCR_001622)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_001622
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elifesciences.org elifesciences.org
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PyMol
DOI: 10.7554/eLife.103159.2
Resource: PyMOL (RRID:SCR_000305)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_000305
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ChimeraX
DOI: 10.7554/eLife.103159.2
Resource: UCSF ChimeraX (RRID:SCR_015872)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_015872
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UCSF Chimera
DOI: 10.7554/eLife.103159.2
Resource: UCSF Chimera (RRID:SCR_004097)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_004097
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cryoSPARC
DOI: 10.7554/eLife.103159.2
Resource: cryoSPARC (RRID:SCR_016501)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_016501
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elifesciences.org elifesciences.org
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Abcam, ab24170
DOI: 10.7554/eLife.103137.2
Resource: (Abcam Cat# ab24170, RRID:AB_775978)
Curator: @areedewitt04
SciCrunch record: RRID:AB_775978
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Cell Signaling Technology, 4240
DOI: 10.7554/eLife.103137.2
Resource: (Cell Signaling Technology Cat# 4240, RRID:AB_11220225)
Curator: @areedewitt04
SciCrunch record: RRID:AB_11220225
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elifesciences.org elifesciences.org
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BrainSight, Rogue Research Inc.
DOI: 10.7554/eLife.102475.2
Resource: Brainsight (RRID:SCR_009539)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_009539
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elifesciences.org elifesciences.org
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GraphPad
DOI: 10.7554/eLife.102417.2
Resource: GraphPad (RRID:SCR_000306)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_000306
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Santa Cruz, sc8002
DOI: 10.7554/eLife.102417.2
Resource: (Santa Cruz Biotechnology Cat# sc-8002, RRID:AB_627558)
Curator: @areedewitt04
SciCrunch record: RRID:AB_627558
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elifesciences.org elifesciences.org
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Illumina HiSeq 2500
DOI: 10.7554/eLife.102166.1
Resource: Illumina HiSeq 2500 System (RRID:SCR_016383)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_016383
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elifesciences.org elifesciences.org
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BigBrain
DOI: 10.7554/eLife.102095.1
Resource: BigBrain (RRID:SCR_001593)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_001593
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elifesciences.org elifesciences.org
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GraphPad Prism
DOI: 10.7554/eLife.101980.1
Resource: GraphPad Prism (RRID:SCR_002798)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_002798
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JAX strain #: 016962
DOI: 10.7554/eLife.101980.1
Resource: (IMSR Cat# JAX_016962,RRID:IMSR_JAX:016962)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:016962
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elifesciences.org elifesciences.org
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GATK v4
DOI: 10.7554/eLife.101882.1
Resource: GATK (RRID:SCR_001876)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_001876
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elifesciences.org elifesciences.org
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LIBSVM
DOI: 10.7554/eLife.101841.1
Resource: LIBSVM (RRID:SCR_010243)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_010243
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Presentation® software
DOI: 10.7554/eLife.101841.1
Resource: Presentation (RRID:SCR_002521)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_002521
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elifesciences.org elifesciences.org
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EEGLAB toolbox 2021.0
DOI: 10.7554/eLife.101802.1
Resource: EEGLAB (RRID:SCR_007292)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_007292
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elifesciences.org elifesciences.org
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FieldTrip Toolbox
DOI: 10.7554/eLife.101262.1
Resource: FieldTrip (RRID:SCR_004849)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_004849
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elifesciences.org elifesciences.org
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Bonsai package BonVision
DOI: 10.7554/eLife.100840.2
Resource: BonVision (RRID:SCR_021534)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_021534
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elifesciences.org elifesciences.org
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MatchIt R
DOI: 10.7554/eLife.100785.3
Resource: MatchIt (RRID:SCR_025618)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_025618
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elifesciences.org elifesciences.org
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Computational Morphometry Toolkit
DOI: 10.7554/eLife.100666.2
Resource: NeuroImaging Tools and Resources Collaboratory (NITRC) (RRID:SCR_003430)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_003430
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DeepLabCut
DOI: 10.7554/eLife.100666.2
Resource: DeepLabCut (RRID:SCR_021391)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_021391
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LabVIEW
DOI: 10.7554/eLife.100666.2
Resource: LabView (RRID:SCR_014325)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_014325
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elifesciences.org elifesciences.org
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Dynamo
DOI: 10.7554/eLife.100335.1
Resource: Dynamo (RRID:SCR_025592)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_025592
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UCSF Chimera
DOI: 10.7554/eLife.100335.1
Resource: UCSF Chimera (RRID:SCR_004097)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_004097
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elifesciences.org elifesciences.org
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Rat Genome Database NMcwiWFsm:HS #13673907
DOI: 10.7554/eLife.90422.2
Resource: RRID:RGD_13673907
Curator: @areedewitt04
SciCrunch record: RRID:RGD_13673907
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elifesciences.org elifesciences.org
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RRID:AB_298079
DOI: 10.7554/eLife.102277
Resource: None
Curator: @sonofthor
SciCrunch record: RRID:AB_298911
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- May 2025
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elifesciences.org elifesciences.org
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RRID:SCR_026986
DOI: 10.7554/eLife.98114
Resource: None
Curator: @scibot
SciCrunch record: RRID:SCR_026986
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RRID:SCR_025480
DOI: 10.7554/eLife.98114
Resource: None
Curator: @scibot
SciCrunch record: RRID:SCR_025480
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RRID:SCR_015656
DOI: 10.7554/eLife.98114
Resource: R package: lmerTest (RRID:SCR_015656)
Curator: @scibot
SciCrunch record: RRID:SCR_015656
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RRID:SCR_026984
DOI: 10.7554/eLife.98114
Resource: None
Curator: @scibot
SciCrunch record: RRID:SCR_026984
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RRID:SCR_026983
DOI: 10.7554/eLife.98114
Resource: None
Curator: @scibot
SciCrunch record: RRID:SCR_026983
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RRID:SCR_015654
DOI: 10.7554/eLife.98114
Resource: R package: lme4 (RRID:SCR_015654)
Curator: @scibot
SciCrunch record: RRID:SCR_015654
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RRID:SCR_026982
DOI: 10.7554/eLife.98114
Resource: None
Curator: @scibot
SciCrunch record: RRID:SCR_026982
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RRID:SCR_026985
DOI: 10.7554/eLife.98114
Resource: None
Curator: @scibot
SciCrunch record: RRID:SCR_026985
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RRID:SCR_001905
DOI: 10.7554/eLife.98114
Resource: R Project for Statistical Computing (RRID:SCR_001905)
Curator: @scibot
SciCrunch record: RRID:SCR_001905
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RRID:SCR_000432
DOI: 10.7554/eLife.98114
Resource: RStudio (RRID:SCR_000432)
Curator: @scibot
SciCrunch record: RRID:SCR_000432
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elifesciences.org elifesciences.org
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RRID:Addgene_100834
DOI: 10.7554/eLife.105422.2
Resource: RRID:Addgene_100834
Curator: @scibot
SciCrunch record: RRID:Addgene_100834
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elifesciences.org elifesciences.org
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RRID:AB_2063534
DOI: 10.7554/eLife.105018
Resource: (Santa Cruz Biotechnology Cat# sc-12721, RRID:AB_2063534)
Curator: @scibot
SciCrunch record: RRID:AB_2063534
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RRID:AB_491015
DOI: 10.7554/eLife.105018
Resource: (Cell Signaling Technology Cat# 9516, RRID:AB_491015)
Curator: @scibot
SciCrunch record: RRID:AB_491015
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RRID:AB_476693
DOI: 10.7554/eLife.105018
Resource: (Sigma-Aldrich Cat# A2066, RRID:AB_476693)
Curator: @scibot
SciCrunch record: RRID:AB_476693
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elifesciences.org elifesciences.org
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RRID:AB_514500
DOI: 10.7554/eLife.100996
Resource: (Roche Cat# 11207733910, RRID:AB_514500)
Curator: @scibot
SciCrunch record: RRID:AB_514500
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RRID:AB_2313908
DOI: 10.7554/eLife.100996
Resource: (Phoenix Pharmaceuticals Cat# H-003-53, RRID:AB_2313908)
Curator: @scibot
SciCrunch record: RRID:AB_2313908
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RRID:AB_514497
DOI: 10.7554/eLife.100996
Resource: (Roche Cat# 11093274910, RRID:AB_514497)
Curator: @scibot
SciCrunch record: RRID:AB_514497
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RRID:AB_840257
DOI: 10.7554/eLife.100996
Resource: (Roche Cat# 11426346910, RRID:AB_840257)
Curator: @scibot
SciCrunch record: RRID:AB_840257
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elifesciences.org elifesciences.org
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Bloomington Stock Center
DOI: 10.7554/eLife.104164.2
Resource: Bloomington Drosophila Stock Center (RRID:SCR_006457)
Curator: @maulamb
SciCrunch record: RRID:SCR_006457
Tags
Annotators
URL
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elifesciences.org elifesciences.org
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plasmid 52961, Addgene
DOI: 10.7554/eLife.101984.2
Resource: RRID:Addgene_52961
Curator: @dhovakimyan1
SciCrunch record: RRID:Addgene_52961
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pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov
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RRID:AB_3076240
DOI: 10.7554/eLife.99410
Resource: (James Trimmer, University of California, Davis Cat# Kv5.1C, RRID:AB_3076240)
Curator: @scibot
SciCrunch record: RRID:AB_3076240
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RRID:SCR_025044
DOI: 10.7554/eLife.99410
Resource: LJPcalc (RRID:SCR_025044)
Curator: @scibot
SciCrunch record: RRID:SCR_025044
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