update to GPLv3

R/bootstrap.R

@@ -1,3 +1,21 @@
+#
+#    sleuth: inspect your RNA-Seq with a pack of kallistos
+#
+#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 # Bootstrap to matrix
 #
 # Takes a \code{kallisto} object and converts the bootstrap results into

R/import.R

@@ -1,3 +1,21 @@
+#
+#    sleuth: inspect your RNA-Seq with a pack of kallistos
+#
+#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 #' @import dplyr
 NULL
 

R/kallisto.R

@@ -1,3 +1,21 @@
+#
+#    sleuth: inspect your RNA-Seq with a pack of kallistos
+#
+#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 #' @export
 print.kallisto <- function(obj) {
   cat("\tkallisto object\n")

R/matrix.R

@@ -1,3 +1,20 @@
+#
+#    sleuth: inspect your RNA-Seq with a pack of kallistos
+#
+#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 #' Convert a sleuth object to matrix
 #'

R/measurement_error.R

@@ -1,3 +1,21 @@
+#
+#    sleuth: inspect your RNA-Seq with a pack of kallistos
+#
+#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 #' Fit a measurement error model
 #'
 #' This function is a wrapper for fitting a measurement error model using

R/misc.R

@@ -1,3 +1,21 @@
+#
+#    sleuth: inspect your RNA-Seq with a pack of kallistos
+#
+#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 #' @export
 get_quantile <- function(data, which_col, lwr, upr, ignore_zeroes = TRUE) {
   data <- as.data.frame(data)

R/model.R

@@ -1,3 +1,21 @@
+#
+#    sleuth: inspect your RNA-Seq with a pack of kallistos
+#
+#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 #' Print sleuth model
 #'
 #' Print a model that has been fit by sleuth

R/plots.R

@@ -1,3 +1,21 @@
+#
+#    sleuth: inspect your RNA-Seq with a pack of kallistos
+#
+#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 #' Mean-variance relationship
 #'
 #' Plot the mean-variance relationship of transcripts as modeled in \code{sleuth}. Each

R/read_write.R

@@ -1,3 +1,21 @@
+#
+#    sleuth: inspect your RNA-Seq with a pack of kallistos
+#
+#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 #' Read a kallisto object from an HDF5 file
 #'
 #' Read a kallisto object from an HDF5 file.

R/shiny.R

@@ -1,3 +1,21 @@
+#
+#    sleuth: inspect your RNA-Seq with a pack of kallistos
+#
+#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 #' Interactive sleuth visualization with Shiny
 #'
 #' Interactive sleuth visualization with Shiny. To exit, type \code{ESC} in R.

R/sleuth.R

@@ -1,3 +1,21 @@
+#
+#    sleuth: inspect your RNA-Seq with a pack of kallistos
+#
+#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 #' Basic row filter
 #'
 #' A basic filter to be used.

R/units.R

@@ -1,3 +1,21 @@
+#
+#    sleuth: inspect your RNA-Seq with a pack of kallistos
+#
+#    Copyright (C) 2015  Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 #' @export
 counts_to_tpm <- function(est_counts, eff_len) {
   stopifnot( length(eff_len) == length(est_counts) )