text: user4595: I am using RStudio Cloud for running velocyto R package. So I have tried to import velocyto file from http://pklab.med.harvard.edu/velocyto/mouseBM/SCG71.loom
  I tried to upload that like so
  
  But saying 
  > SCG71 <- read.table("/cloud/project/SCG71.loom", header=TRUE, quote="\"")
  Error in make.names(col.names, unique = TRUE) : 
    invalid multibyte string at '<89>HDF'
  In addition: There were 19 warnings (use warnings() to see them)
  
  Can you help me in very initial of velocyto R?
  
  user3541: This seems to be an encoding problem (certain characters not being recognized), see this, this and also this. Probably the file "/cloud/project/SCG71.loom" is encoded with a format that is not included in your "locale".
  Check the output of Sys.getlocale() and see if your input file's encoding is listed. If not, you will need to try something like Sys.setlocale("LC_CTYPE", "en_US.UTF-8") or Sys.setlocale("LC_ALL", "English") (see the third link for details).
  
  user6437: Velocyto.R
  I'm not sure that your issues is from RStudio cloud but more about how you are trying to open the file. The file that you are trying to import is not a velocyto file but a .loom file that can be open using the velocyto.R package. 
  I'm not very familiar with this kind of of .loom file but on the velocyto.R tutorial, it is specified to do the following: 
  library(velocyto.R)
  ldat <- read.loom.matrices("SCG71.loom")
  
  And you have the following file structures:
  > str(ldat)
  List of 3
   $ spliced  :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
    .. ..@ i       : int [1:2822201] 74 130 178 192 202 223 225 258 353 418 ...
    .. ..@ p       : int [1:6668] 0 464 786 1469 2502 3290 3760 4974 5388 5659 ...
    .. ..@ Dim     : int [1:2] 24421 6667
    .. ..@ Dimnames:List of 2
    .. .. ..$ : chr [1:24421] "Xkr4" "Rp1" "Sox17" "Mrpl15" ...
    .. .. ..$ : chr [1:6667] "SCG71:AAACGATCCTACTTGT" "SCG71:AAACACTACGTAGAAG" "SCG71:AAACACGGCATCGCAG" "SCG71:AAACAAACAGCAGAAC" ...
    .. ..@ x       : num [1:2822201] 1 1 1 1 1 1 1 1 1 4 ...
    .. ..@ factors : list()
   $ unspliced:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
    .. ..@ i       : int [1:528048] 61 100 339 352 377 445 465 528 617 758 ...
    .. ..@ p       : int [1:6668] 0 115 188 283 431 580 696 994 1127 1232 ...
    .. ..@ Dim     : int [1:2] 24421 6667
    .. ..@ Dimnames:List of 2
    .. .. ..$ : chr [1:24421] "Xkr4" "Rp1" "Sox17" "Mrpl15" ...
    .. .. ..$ : chr [1:6667] "SCG71:AAACGATCCTACTTGT" "SCG71:AAACACTACGTAGAAG" "SCG71:AAACACGGCATCGCAG" "SCG71:AAACAAACAGCAGAAC" ...
    .. ..@ x       : num [1:528048] 1 3 1 1 1 1 1 1 1 1 ...
    .. ..@ factors : list()
   $ ambiguous:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
    .. ..@ i       : int [1:47846] 11915 13649 13830 15638 18068 19585 23490 24345 8142 8767 ...
    .. ..@ p       : int [1:6668] 0 8 13 25 42 56 64 87 97 100 ...
    .. ..@ Dim     : int [1:2] 24421 6667
    .. ..@ Dimnames:List of 2
    .. .. ..$ : chr [1:24421] "Xkr4" "Rp1" "Sox17" "Mrpl15" ...
    .. .. ..$ : chr [1:6667] "SCG71:AAACGATCCTACTTGT" "SCG71:AAACACTACGTAGAAG" "SCG71:AAACACGGCATCGCAG" "SCG71:AAACAAACAGCAGAAC" ...
    .. ..@ x       : num [1:47846] 2 1 1 1 1 2 1 2 1 1 ...
    .. ..@ factors : list()
  
  Alternative 1 - LoomExperiment
  On bioconductor, you can also find LoomExperiment. On my computer, once I get it install, I was able to load your SCG71.loom file using:
  library(LoomExperiment)
  scle <- import("SCG71.loom",type = "LoomExperiment", rownames_attr = NULL, colnames_attr = NULL)
  
  Then, you can find the output here:
  > head(scle)
  class: LoomExperiment 
  dim: 6 6667 
  metadata(4): chunks creation_date velocyto.__version__ velocyto.logic
  assays(4): matrix ambiguous spliced unspliced
  rownames: NULL
  rowData names(6): Accession Chromosome ... Start Strand
  colnames: NULL
  colData names(1): CellID
  rowGraphs(0): NULL
  colGraphs(0): NULL
  
  You can then load some data
  > scle$CellID[c(1:5)]
  [1] "SCG71:AAACGATCCTACTTGT" "SCG71:AAACACTACGTAGAAG" "SCG71:AAACACGGCATCGCAG"
  [4] "SCG71:AAACAAACAGCAGAAC" "SCG71:AAACAAACTTTGGGAG"
  
  After that, I don't know what to do with that but I think your issue of importing a datafile is because you don't have the right package to open it. 
  Alternative - using LoomR
  Alternatively, you can also install the package loomR and then enter:
  library(loomR)
  lfile = connect(filename = "SCG71.loom", mode = "r+")
  
  And you get the output:
  > lfile
  Class: loom
  Filename: /***my_directory***/SCG71.loom
  Access type: H5F_ACC_RDWR
  Attributes: creation_date, chunks, velocyto.__version__, velocyto.logic, version
  Listing:
         name    obj_type dataset.dims dataset.type_class
    col_attrs   H5I_GROUP         <NA>               <NA>
   col_graphs   H5I_GROUP         <NA>               <NA>
       layers   H5I_GROUP         <NA>               <NA>
       matrix H5I_DATASET 6667 x 24421          H5T_FLOAT
    row_attrs   H5I_GROUP         <NA>               <NA>
   row_graphs   H5I_GROUP         <NA>               <NA>
  
  Then, for manipulating these files, you should refer to their tutorial (it's beyond my skills and the scope of your question).
  Hope it helps you to figure the solution of your question
  
original_text: 4595: <p>I am using RStudio Cloud for running velocyto R package. So I have tried to import velocyto file from <a href="http://pklab.med.harvard.edu/velocyto/mouseBM/SCG71.loom" rel="nofollow noreferrer">http://pklab.med.harvard.edu/velocyto/mouseBM/SCG71.loom</a></p>
  
  <p>I tried to upload that like so</p>
  
  <p><a href="https://i.stack.imgur.com/rsi7N.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/rsi7N.png" alt="enter image description here"></a></p>
  
  <p>But saying </p>
  
  <pre><code>&gt; SCG71 &lt;- read.table("/cloud/project/SCG71.loom", header=TRUE, quote="\"")
  Error in make.names(col.names, unique = TRUE) : 
    invalid multibyte string at '&lt;89&gt;HDF'
  In addition: There were 19 warnings (use warnings() to see them)
  </code></pre>
  
  <p>Can you help me in very initial of velocyto R?</p>
   3541: <p>This seems to be an encoding problem (certain characters not being recognized), see <a href="https://stackoverflow.com/questions/14363085/invalid-multibyte-string-in-read-csv/29586283">this</a>, <a href="https://stackoverflow.com/questions/4993837/r-invalid-multibyte-string">this</a> and also <a href="https://www.r-bloggers.com/web-scraping-and-invalid-multibyte-string/" rel="nofollow noreferrer">this</a>. Probably the file <code>"/cloud/project/SCG71.loom"</code> is encoded with a format that is not included in your "locale".</p>
  
  <p>Check the output of <code>Sys.getlocale()</code> and see if your input file's encoding is listed. If not, you will need to try something like <code>Sys.setlocale("LC_CTYPE", "en_US.UTF-8")</code> or <code>Sys.setlocale("LC_ALL", "English")</code> (see the third link for details).</p>
   6437: <p><strong>Velocyto.R</strong></p>
  
  <p>I'm not sure that your issues is from RStudio cloud but more about how you are trying to open the file. The file that you are trying to import is not a <code>velocyto</code> file but a <code>.loom</code> file that can be open using the <code>velocyto.R</code> package. </p>
  
  <p>I'm not very familiar with this kind of of <code>.loom</code> file but on the <a href="http://pklab.med.harvard.edu/velocyto/notebooks/R/DG1.nb.html" rel="nofollow noreferrer"><code>velocyto.R</code></a> tutorial, it is specified to do the following: </p>
  
  <pre class="lang-r prettyprint-override"><code>library(velocyto.R)
  ldat &lt;- read.loom.matrices("SCG71.loom")
  </code></pre>
  
  <p>And you have the following file structures:</p>
  
  <pre class="lang-r prettyprint-override"><code>&gt; str(ldat)
  List of 3
   $ spliced  :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
    .. ..@ i       : int [1:2822201] 74 130 178 192 202 223 225 258 353 418 ...
    .. ..@ p       : int [1:6668] 0 464 786 1469 2502 3290 3760 4974 5388 5659 ...
    .. ..@ Dim     : int [1:2] 24421 6667
    .. ..@ Dimnames:List of 2
    .. .. ..$ : chr [1:24421] "Xkr4" "Rp1" "Sox17" "Mrpl15" ...
    .. .. ..$ : chr [1:6667] "SCG71:AAACGATCCTACTTGT" "SCG71:AAACACTACGTAGAAG" "SCG71:AAACACGGCATCGCAG" "SCG71:AAACAAACAGCAGAAC" ...
    .. ..@ x       : num [1:2822201] 1 1 1 1 1 1 1 1 1 4 ...
    .. ..@ factors : list()
   $ unspliced:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
    .. ..@ i       : int [1:528048] 61 100 339 352 377 445 465 528 617 758 ...
    .. ..@ p       : int [1:6668] 0 115 188 283 431 580 696 994 1127 1232 ...
    .. ..@ Dim     : int [1:2] 24421 6667
    .. ..@ Dimnames:List of 2
    .. .. ..$ : chr [1:24421] "Xkr4" "Rp1" "Sox17" "Mrpl15" ...
    .. .. ..$ : chr [1:6667] "SCG71:AAACGATCCTACTTGT" "SCG71:AAACACTACGTAGAAG" "SCG71:AAACACGGCATCGCAG" "SCG71:AAACAAACAGCAGAAC" ...
    .. ..@ x       : num [1:528048] 1 3 1 1 1 1 1 1 1 1 ...
    .. ..@ factors : list()
   $ ambiguous:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
    .. ..@ i       : int [1:47846] 11915 13649 13830 15638 18068 19585 23490 24345 8142 8767 ...
    .. ..@ p       : int [1:6668] 0 8 13 25 42 56 64 87 97 100 ...
    .. ..@ Dim     : int [1:2] 24421 6667
    .. ..@ Dimnames:List of 2
    .. .. ..$ : chr [1:24421] "Xkr4" "Rp1" "Sox17" "Mrpl15" ...
    .. .. ..$ : chr [1:6667] "SCG71:AAACGATCCTACTTGT" "SCG71:AAACACTACGTAGAAG" "SCG71:AAACACGGCATCGCAG" "SCG71:AAACAAACAGCAGAAC" ...
    .. ..@ x       : num [1:47846] 2 1 1 1 1 2 1 2 1 1 ...
    .. ..@ factors : list()
  </code></pre>
  
  <p><strong>Alternative 1 - LoomExperiment</strong></p>
  
  <p>On bioconductor, you can also find <a href="https://bioconductor.org/packages/release/bioc/vignettes/LoomExperiment/inst/doc/LoomExperiment.html#available-methods-for-the-loomexperiment" rel="nofollow noreferrer"><code>LoomExperiment</code></a>. On my computer, once I get it install, I was able to load your <code>SCG71.loom</code> file using:</p>
  
  <pre class="lang-r prettyprint-override"><code>library(LoomExperiment)
  scle &lt;- import("SCG71.loom",type = "LoomExperiment", rownames_attr = NULL, colnames_attr = NULL)
  </code></pre>
  
  <p>Then, you can find the output here:</p>
  
  <pre class="lang-r prettyprint-override"><code>&gt; head(scle)
  class: LoomExperiment 
  dim: 6 6667 
  metadata(4): chunks creation_date velocyto.__version__ velocyto.logic
  assays(4): matrix ambiguous spliced unspliced
  rownames: NULL
  rowData names(6): Accession Chromosome ... Start Strand
  colnames: NULL
  colData names(1): CellID
  rowGraphs(0): NULL
  colGraphs(0): NULL
  </code></pre>
  
  <p>You can then load some data</p>
  
  <pre class="lang-r prettyprint-override"><code>&gt; scle$CellID[c(1:5)]
  [1] "SCG71:AAACGATCCTACTTGT" "SCG71:AAACACTACGTAGAAG" "SCG71:AAACACGGCATCGCAG"
  [4] "SCG71:AAACAAACAGCAGAAC" "SCG71:AAACAAACTTTGGGAG"
  </code></pre>
  
  <p>After that, I don't know what to do with that but I think your issue of importing a datafile is because you don't have the right package to open it. </p>
  
  <p><strong>Alternative - using LoomR</strong></p>
  
  <p>Alternatively, you can also install the package <a href="https://satijalab.org/loomR/loomR_tutorial.html" rel="nofollow noreferrer"><code>loomR</code></a> and then enter:</p>
  
  <pre class="lang-r prettyprint-override"><code>library(loomR)
  lfile = connect(filename = "SCG71.loom", mode = "r+")
  </code></pre>
  
  <p>And you get the output:</p>
  
  <pre class="lang-r prettyprint-override"><code>&gt; lfile
  Class: loom
  Filename: /***my_directory***/SCG71.loom
  Access type: H5F_ACC_RDWR
  Attributes: creation_date, chunks, velocyto.__version__, velocyto.logic, version
  Listing:
         name    obj_type dataset.dims dataset.type_class
    col_attrs   H5I_GROUP         &lt;NA&gt;               &lt;NA&gt;
   col_graphs   H5I_GROUP         &lt;NA&gt;               &lt;NA&gt;
       layers   H5I_GROUP         &lt;NA&gt;               &lt;NA&gt;
       matrix H5I_DATASET 6667 x 24421          H5T_FLOAT
    row_attrs   H5I_GROUP         &lt;NA&gt;               &lt;NA&gt;
   row_graphs   H5I_GROUP         &lt;NA&gt;               &lt;NA&gt;
  </code></pre>
  
  <p>Then, for manipulating these files, you should refer to their tutorial (it's beyond my skills and the scope of your question).</p>
  
  <p>Hope it helps you to figure the solution of your question</p>
  