Shreffler R course

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ShreffLab Internal R analysis course -- 2014

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Course overview

This is the ShreffLab's introductory course on R analysis. The course design and materials borrow heavily from other sources, including the Clarkson University tutorial, the introduction by Emmanuel Paradis, and others that are cited in the materials and are available R_Statistics here.

A couple of additional resources:

Recent updates to the course

19 April 2018

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XROMM‎‎ (8 changes | history) . . (+1,185). . [Aolsen‎ (8×)]

     

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(cur | prev) . . (+57). . Aolsen (talk | contribs)

     

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(cur | prev) . . (+328). . Aolsen (talk | contribs)

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Silver: 2018 Meeting Schedule‎‎ (4 changes | history) . . (+6). . [PamSilver‎ (4×)]

     

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(cur | prev) . . (+2). . PamSilver (talk | contribs) (June)

     

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(cur | prev) . . (+1). . PamSilver (talk | contribs) (May)

     

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(cur | prev) . . (+3). . PamSilver (talk | contribs) (April)

     11:26 (Move log) . . Aolsen (talk | contribs) moved page Xromm to XROMM(Acronym looks better in caps)

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Xromm‎‎ (2 changes | history) . . (+708). . [Aolsen‎ (2×)]

     

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(cur | prev) . . (+1,475). . Aolsen (talk | contribs) (Created page with "{{back to protocols}} X-ray Reconstruction of Moving Morphology (XROMM) is a 3D imaging technology, developed at Brown University, for visualizing rapid skeletal movement in v...")

     08:40  Taylor:Publications‎ (diff | hist) . . (+18). . Lynne S. Taylor (talk | contribs) (PUBLICATIONS)
     07:22  Lee:JC‎ (diff | hist) . . (+166). . Wooin Lee (talk | contribs) (Lab meeting schedule)

18 April 2018

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X-Lab‎‎ (4 changes | history) . . (0). . [ChanEngr‎ (4×)]

     

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User:Korey Griffin‎‎ (2 changes | history) . . (+32). . [Korey Griffin‎ (2×)]

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(cur | prev) . . (-47). . Korey Griffin (talk | contribs) (Contact)

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(cur | prev) . . (+79). . Korey Griffin (talk | contribs) (Empirical Resources)

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User:Johannes Stuttmann‎‎ (3 changes | history) . . (+4,407). . [Johannes Stuttmann‎ (3×)]

     

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     13:02  Hydrochloric acid‎ (diff | hist) . . (+1). . Yar (talk | contribs) (typing error from user email)

     12:52 

(User creation log). .

[Yar‎ (2×)]

     

12:52

. . User account Ally B (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

     

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. . User account Jakob (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

     12:46 

BIOL478/S18:Microarray Data Analysis‎‎ (21 changes | history) . . (+7,513). . [Kam D. Dahlquist‎ (21×)]

     

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(cur | prev) . . (-70). . Kam D. Dahlquist (talk | contribs) (Gridding and Generating Intensity Data: remove old Brightspace link)

     

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(cur | prev) . . (+1). . Kam D. Dahlquist (talk | contribs) (GenePix Pro Protocol (Steps 1-3): fix Brightspace link to raw data)

     

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(cur | prev) . . (+1,241). . Kam D. Dahlquist (talk | contribs) (Before We Begin: add section on lab notebook)

     

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(cur | prev) . . (0). . Kam D. Dahlquist (talk | contribs) (Background: fix list formatting)

     

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(cur | prev) . . (+108). . Kam D. Dahlquist (talk | contribs) (Background: add GRNsight)

     

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(cur | prev) . . (+3,845). . Kam D. Dahlquist (talk | contribs) (Identifying regulatory transcription factors responsible for observed changes in gene expression (step 10): paste in GRNsight instructions)

     

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(cur | prev) . . (+3,072). . Kam D. Dahlquist (talk | contribs) (Identifying regulatory transcription factors responsible for observed changes in gene expression (step 10): paste in protocol from Biomath modeling, modify for HMO1)

     

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(cur | prev) . . (+114). . Kam D. Dahlquist (talk | contribs) (Clustering and GO Term Enrichment with stem (steps 7-8): add section for step 10)

     

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(cur | prev) . . (-751). . Kam D. Dahlquist (talk | contribs) (Clustering and GO Term Enrichment with stem (steps 7-8): delete comment, emphasize to unzip)

     

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(cur | prev) . . (0). . Kam D. Dahlquist (talk | contribs) (Modified t test for each timepoint: fix formula)

     

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(cur | prev) . . (+52). . Kam D. Dahlquist (talk | contribs) (Sanity Check: Number of genes significantly changed: add label to link)

     

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(cur | prev) . . (+29). . Kam D. Dahlquist (talk | contribs) (Sanity Check: Number of genes significantly changed: add link to xkcd comic)

     

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(cur | prev) . . (-360). . Kam D. Dahlquist (talk | contribs) (replace opi1 with hmo1)

     

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(cur | prev) . . (+18). . Kam D. Dahlquist (talk | contribs) (replace wt with dHMO1)

     

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(cur | prev) . . (+36). . Kam D. Dahlquist (talk | contribs) (Modified t test for each timepoint: replace wt with dHMO1)

     

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(cur | prev) . . (-22). . Kam D. Dahlquist (talk | contribs) (Looking at the raw data: fix links to SGD)

     

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(cur | prev) . . (+3). . Kam D. Dahlquist (talk | contribs) (Downloading the Data: change to hmo1)

     

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(cur | prev) . . (+35). . Kam D. Dahlquist (talk | contribs) (Statistical Analysis (Step 6): change to delta-hmo1)

     

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(cur | prev) . . (+61). . Kam D. Dahlquist (talk | contribs) (GenePix Pro Protocol (Steps 1-3): note that this will be demo'd, change opi1 to hmo1)

     

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(cur | prev) . . (+27). . Kam D. Dahlquist (talk | contribs) (Background: steps 1-3 done for you)

     

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(cur | prev) . . (+74). . Kam D. Dahlquist (talk | contribs) (Background: add link for YEASTRACT)