Release 3.6

Author: uchicago-handena

REDItools3.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: REDItools3
-Version: 3.5
+Version: 3.6
 Author: Ernesto Picardi
 Author-email: Adam Handen <adam.handen@gmail.com>
 License-Expression: GPL-3.0-or-later
@@ -48,12 +48,12 @@ The output is a tab separated table with these columns:
 | Position      | Position in the region |
 | Reference     | Base from the reference sequence |
 | Strand        | DNA strand (+, -, or \*) |
-| Coverage-q30  | How many reads had a quality of at least 30 |
+| Coverage      | How many reads passed quality thresholds |
 | MeanQ         | Mean read quality |
 | BaseCount[A,C,G,T] | Total count of each base found |
 | AllSubs       | All the detected substitutions |
 | Frequency     | Ratio of non-reference bases to reference bases |
-| gCoverage-q30 | Genomic Coverage-q30 (see `annotate`) |
+| gCoverage     | Genomic Coverage (see `annotate`) |
 | gMeanQ        | Genomic MeanQ (see `annotate`) |
 | gBaseCount[A,C,G,T] | Genomic BaseCount (see `annotate`) |
 | gAllSubs      | Genomic variants (see `annotate`) |
@@ -70,21 +70,21 @@ of the first file with positional matches from the second.
 
 For example, this RNA file:
 ```
-Region	Position	Reference	Strand	Coverage-q30	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage-q30	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency
+Region	Position	Reference	Strand	Coverage	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency
 chr1	1115715	C	*	2	38.00	[0, 2, 0, 0]	-	0.00	-	-	-	-	-
 chr1	1115716	A	*	2	38.00	[2, 0, 0, 0]	-	0.00	-	-	-	-	-
 ```
 
 With this DNA file:
 ```
-Region	Position	Reference	Strand	Coverage-q30	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage-q30	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency
+Region	Position	Reference	Strand	Coverage	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency
 chr1	1115716	A	*	2	38.00	[2, 0, 0, 0]	-	0.00	-	-	-	-	-
 chr1	1115717	C	*	2	38.00	[0, 2, 0, 0]	-	0.00	-	-	-	-	-
 ```
 
 Produces:
 ```
-Region	Position	Reference	Strand	Coverage-q30	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage-q30	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency
+Region	Position	Reference	Strand	Coverage	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency
 chr1	1115715	C	*	2	38.00	[0, 2, 0, 0]	-	0.00	-	-	-	-	-
 chr1    1115716 A       *       2       38.00   [2, 0, 0, 0]    -       0.00    2       38.00   [2, 0, 0, 0]    -       0.00
 ```
@@ -97,3 +97,8 @@ Compute RNA editing index from reditools `analyze` output
 ([PMDI: 31636457](https://pubmed.ncbi.nlm.nih.gov/31636457/)).
 The `index` tool computes the editing indices for all possible variants, not
 just A-to-I (listed as A-G in the output).
+
+# Citing and Credit
+Please cite the following papers when using REDItools3
+1. Fonzino A, Mazzacuva PL, Handen A, Silvestris DA, Arnold A, Pecori R, Pesole G, Picardi E. REDInet: a temporal convolutional network-based classifier for A-to-I RNA editing detection harnessing million known events. Brief Bioinform. 2025 Mar 4;26(2):bbaf107. doi: 10.1093/bib/bbaf107. PMID: 40112338; PMCID: PMC11924403.
+2. Picardi E, Pesole G. REDItools: high-throughput RNA editing detection made easy. Bioinformatics. 2013 Jul 15;29(14):1813-4. doi: 10.1093/bioinformatics/btt287. Epub 2013 Jun 5. PMID: 23742983.

dist/reditools3-3.5.tar.gz

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "REDItools3"
-version = "v3.5"
+version = "v3.6"
 license = "GPL-3.0-or-later"
 authors = [
   { name="Ernesto Picardi" },