tepr

Transcription Elongation Profiling

v1.1.15 · Mar 6, 2026 · GPL-3

Description

The general principle relies on calculating the cumulative signal of nascent RNA sequencing over the gene body of any given gene or transcription unit. 'tepr' can identify transcription attenuation sites by comparing profile to a null model which assumes uniform read density over the entirety of the transcription unit. It can also identify increased or diminished transcription attenuation by comparing two conditions. Besides rigorous statistical testing and high sensitivity, a major feature of 'tepr' is its ability to provide the elongation pattern of each individual gene, including the position of the main attenuation point when such a phenomenon occurs. Using 'tepr', users can visualize and refine genome-wide aggregated analyses of elongation patterns to robustly identify effects specific to subsets of genes. These metrics are suitable for internal comparisons (between genes in each condition) and for studying elongation of the same gene in different conditions or comparing it to a perfect theoretical uniform elongation.

Downloads

555

Last 30 days

6603rd

1.7K

Last 90 days

3.8K

Last year

Trend: +8.8% (30d vs prior 30d)

CRAN Check Status

13 OK

Show all 13 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	OK	521.7s
r-devel-linux-x86_64-debian-gcc	OK	398.9s
r-devel-linux-x86_64-fedora-clang	OK	729.9s
r-devel-linux-x86_64-fedora-gcc	OK	895.7s
r-devel-windows-x86_64	OK	489s
r-oldrel-macos-arm64	OK	134s
r-oldrel-macos-x86_64	OK	445s
r-oldrel-windows-x86_64	OK	653s
r-patched-linux-x86_64	OK	506.1s
r-release-linux-x86_64	OK
r-release-macos-arm64	OK	145s
r-release-macos-x86_64	OK	489s
r-release-windows-x86_64	OK	483s

Check History

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 24, 2026

ERROR 11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 19, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Nicolas Descostes <nicolas.descostes@gmail.com>’

Additional repositories with no packages:
  https://bioconductor.org/packages/3.22/bioc

ERROR r-devel-linux-x86_64-debian-gcc

examples

Running examples in ‘tepr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: retrievechrom
> ### Title: Retrieve chromosome lengths and information for a specified
> ###   genome.
> 
...[truncated]...
 lengths
Error in retrievechrom(genomename = "hg19", verbose = TRUE) : 
[tepr] Error: Genome not found.
  'hg19' not found via SeqinfoForUCSCGenome.
  Check spelling or UCSC availability.
  Alternatively, provide 'chromtab' directly.
Execution halted

NOTE 12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 17, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Nicolas Descostes <nicolas.descostes@gmail.com>’

Additional repositories with no packages:
  https://bioconductor.org/packages/3.22/bioc

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 14, 2026

ERROR 11 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Jun 7, 2026

ERROR r-devel-linux-x86_64-debian-gcc

examples

Running examples in ‘tepr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: retrievechrom
> ### Title: Retrieve chromosome lengths and information for a specified
> ###   genome.
> 
...[truncated]...
 lengths
Error in retrievechrom(genomename = "hg19", verbose = TRUE) : 
[tepr] Error: Genome not found.
  'hg19' not found via SeqinfoForUCSCGenome.
  Check spelling or UCSC availability.
  Alternatively, provide 'chromtab' directly.
Execution halted

ERROR r-release-linux-x86_64

examples

Running examples in ‘tepr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: retrievechrom
> ### Title: Retrieve chromosome lengths and information for a specified
> ###   genome.
> 
...[truncated]...
 lengths
Error in retrievechrom(genomename = "hg19", verbose = TRUE) : 
[tepr] Error: Genome not found.
  'hg19' not found via SeqinfoForUCSCGenome.
  Check spelling or UCSC availability.
  Alternatively, provide 'chromtab' directly.
Execution halted

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 3, 2026

ERROR 11 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE May 30, 2026

ERROR r-devel-linux-x86_64-debian-clang

examples

Running examples in ‘tepr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: retrievechrom
> ### Title: Retrieve chromosome lengths and information for a specified
> ###   genome.
> 
...[truncated]...
 lengths
Error in retrievechrom(genomename = "hg19", verbose = TRUE) : 
[tepr] Error: Genome not found.
  'hg19' not found via SeqinfoForUCSCGenome.
  Check spelling or UCSC availability.
  Alternatively, provide 'chromtab' directly.
Execution halted

ERROR r-oldrel-windows-x86_64

examples

Running examples in 'tepr-Ex.R' failed
The error most likely occurred in:

> ### Name: retrievechrom
> ### Title: Retrieve chromosome lengths and information for a specified
> ###   genome.
> ### Aliases: retrievechrom
> 
> ### ** Examples
> 
> # Thi
...[truncated]...
 lengths
Error in retrievechrom(genomename = "hg19", verbose = TRUE) : 
[tepr] Error: Genome not found.
  'hg19' not found via SeqinfoForUCSCGenome.
  Check spelling or UCSC availability.
  Alternatively, provide 'chromtab' directly.
Execution halted

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 10, 2026

ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE May 3, 2026

ERROR r-release-linux-x86_64

package dependencies

Package required but not available: ‘rtracklayer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 1, 2026

ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 28, 2026

ERROR r-oldrel-windows-x86_64

examples

Running examples in 'tepr-Ex.R' failed
The error most likely occurred in:

> ### Name: retrievechrom
> ### Title: Retrieve chromosome lengths and information for a specified
> ###   genome.
> ### Aliases: retrievechrom
> 
> ### ** Examples
> 
> # Thi
...[truncated]...
 lengths
Error in retrievechrom(genomename = "hg19", verbose = TRUE) : 
[tepr] Error: Genome not found.
  'hg19' not found via SeqinfoForUCSCGenome.
  Check spelling or UCSC availability.
  Alternatively, provide 'chromtab' directly.
Execution halted

OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026

NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

NOTE r-oldrel-macos-arm64

installed package size

installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   2.6Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   2.6Mb

Dependency Network

Version History

9 tracked

new 1.1.15 Mar 10, 2026

updated 1.1.15 ← 1.1.14 diff Mar 5, 2026

updated 1.1.14 ← 1.1.13 diff Jan 27, 2026

updated 1.1.13 ← 1.1.12 diff Dec 11, 2025

updated 1.1.12 ← 1.1.11 diff Nov 3, 2025

updated 1.1.11 ← 1.1.10 diff Oct 23, 2025

updated 1.1.10 ← 1.1.9 diff Sep 2, 2025

updated 1.1.9 ← 1.1.8 diff Aug 18, 2025

new 1.1.8 Apr 21, 2025