smithlabcode/ribotricer issues and pull requests

#164 - Where to specify an output folder

Issue - State: closed - Opened by pkohvaei 3 months ago - 1 comment

#163 - TYPICAL_OFFSET = 12

Issue - State: closed - Opened by fenghuawei 4 months ago - 1 comment

#162 - Handling read-level P-Site offsets

Issue - State: closed - Opened by mosi223 6 months ago - 6 comments

#161 - Unannotated ORFs

Issue - State: closed - Opened by singhbhavya 7 months ago - 10 comments

#160 - Question about Multi-Mappers

Issue - State: closed - Opened by singhbhavya 7 months ago - 1 comment

#159 - Question about handling of non-unique alignments

Issue - State: closed - Opened by mosi223 7 months ago - 2 comments

#158 - Fixing linter errors

Pull Request - State: closed - Opened by andrewdavidsmith 8 months ago - 1 comment

#157 - Peptide search from ORFs.

Issue - State: closed - Opened by bshim181 8 months ago - 1 comment

#156 - ORF Profile

Issue - State: closed - Opened by bshim181 8 months ago - 1 comment

#155 - Add new meta_min_reads CLI param

Pull Request - State: closed - Opened by pinin4fjords 8 months ago - 3 comments

#154 - Control over minimum coverage + better error messages

Issue - State: closed - Opened by pinin4fjords 8 months ago - 2 comments

#153 - [BUG] speficying unstranded data ('no') leads to error

Issue - State: open - Opened by pinin4fjords 9 months ago - 3 comments

#152 - Prepare ORFs step

Issue - State: closed - Opened by bshim181 10 months ago - 2 comments

#151 - Translation initiation analysis

Issue - State: closed - Opened by colin986 10 months ago - 1 comment

#150 - Could not solve for environment specs: click-help-colors >=0.3 , which does not exist (perhaps a missing channel)

Issue - State: closed - Opened by spencer411 10 months ago - 1 comment

#149 - Unstranded Library

Issue - State: closed - Opened by bshim181 11 months ago - 1 comment

#148 - About the read density in the output file

Issue - State: closed - Opened by lbwfff 11 months ago - 1 comment

#147 - What does the ORF_ID represent?

Issue - State: closed - Opened by carajj 12 months ago - 1 comment

#146 - [BUG]

Issue - State: closed - Opened by fork16 about 1 year ago - 1 comment

#145 - ORF Annotations

Issue - State: open - Opened by bshim181 about 1 year ago - 1 comment

#144 - I have confuse about the profile column from translating_ORFs.tsv

Issue - State: closed - Opened by fork16 about 1 year ago - 1 comment

#143 - Ribotricer Output

Issue - State: closed - Opened by bshim181 about 1 year ago - 5 comments

#142 - Translation of ORFs

Issue - State: closed - Opened by SuiyueWestlake over 1 year ago - 1 comment

#141 - Ribotricer Output

Issue - State: closed - Opened by bshim181 over 1 year ago - 1 comment

#140 - Empty result in first step (Preparing candidate ORFs)

Issue - State: closed - Opened by SuiyueWestlake over 1 year ago - 4 comments

#139 - Ribotricer Output

Issue - State: closed - Opened by bshim181 over 1 year ago - 3 comments

#138 - [BUG] Weird results when using profile from Ribotricer output ?

Issue - State: closed - Opened by polklin over 1 year ago - 2 comments

#137 - Question on prepare-orfs "--longest" flag

Issue - State: closed - Opened by ericmalekos almost 2 years ago - 1 comment

#136 - Trouble installing with bioconda [BUG]

Issue - State: closed - Opened by ericmalekos almost 2 years ago - 2 comments

#135 - ORF_ID naming confusion

Issue - State: closed - Opened by Tim-Yu almost 2 years ago - 5 comments

#134 - Unable to run learn-cutoff function

Issue - State: closed - Opened by bsms9e0n almost 2 years ago - 16 comments

#133 - about 3nt periodicity output

Issue - State: closed - Opened by Jiahuan90 about 2 years ago - 4 comments

#132 - Bump matplotlib from 3.5.3 to 3.6.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#131 - Bump tqdm from 4.64.0 to 4.64.1

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#130 - About definition of ORFs

Issue - State: closed - Opened by Jiahuan90 over 2 years ago - 1 comment

#129 - Bump matplotlib from 3.5.2 to 3.5.3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#128 - Bump pyfaidx from 0.7.0 to 0.7.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#127 - Bump pyfaidx from 0.6.4 to 0.7.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#126 - Bump pysam from 0.19.0 to 0.19.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#125 - Option to include multimapping reads?

Issue - State: closed - Opened by PVlasov93 over 2 years ago - 1 comment

#124 - Bump matplotlib from 3.5.1 to 3.5.2

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#123 - Bump click from 8.1.2 to 8.1.3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#122 - p-site offsets and metagene profiles

Issue - State: open - Opened by p-levy over 2 years ago - 5 comments

#121 - Bump tqdm from 4.63.1 to 4.64.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#120 - Bump click from 8.1.0 to 8.1.2

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#119 - Bump click from 8.1.0 to 8.1.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#118 - Bump pysam from 0.18.0 to 0.19.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#117 - Bump click from 8.0.4 to 8.1.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#116 - Bump tqdm from 4.62.3 to 4.63.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#115 - About the length of reads

Issue - State: closed - Opened by lbwfff over 2 years ago - 3 comments

#114 - Bump tqdm from 4.62.3 to 4.63.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#113 - Bump click from 8.0.3 to 8.0.4

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#112 - Bump pandas from 1.3.5 to 1.4.1

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#111 - Bump scipy from 1.7.3 to 1.8.0

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#110 - Bump numpy from 1.21.5 to 1.22.2

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#109 - Bump pyfaidx from 0.6.3.1 to 0.6.4

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#108 - RPF counts to TPM conversion

Issue - State: closed - Opened by HiteshKore almost 3 years ago - 2 comments

#107 - Bump pandas from 1.3.5 to 1.4.0

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#106 - Bump numpy from 1.21.5 to 1.22.1

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#105 - Bump numpy from 1.21.5 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#104 - Bump numpy from 1.21.4 to 1.21.5

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#103 - Internal ORFs

Issue - State: open - Opened by annebresciani almost 3 years ago - 2 comments

#102 - Allow input of already p-shifted reads (bigwig)

Issue - State: closed - Opened by Roleren almost 3 years ago - 4 comments

#101 - Bump pandas from 1.3.4 to 1.3.5

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#100 - Bump matplotlib from 3.5.0 to 3.5.1

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#99 - Bump scipy from 1.7.2 to 1.7.3

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#98 - Bump pysam from 0.17.0 to 0.18.0

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#97 - Bump matplotlib from 3.4.3 to 3.5.0

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#96 - Bump scipy from 1.7.1 to 1.7.2

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#95 - Bump numpy from 1.21.3 to 1.21.4

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#94 - Bump pyfaidx from 0.6.2 to 0.6.3.1

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#93 - Error while processing the Ribo-Seq data using transcriptome based index

Issue - State: closed - Opened by HiteshKore about 3 years ago - 2 comments

#92 - Confusion about orf information

Issue - State: closed - Opened by lbwfff about 3 years ago - 12 comments

#91 - Queries regarding Ribo-Seq analysis

Issue - State: closed - Opened by HiteshKore about 3 years ago - 7 comments

#90 - Bump numpy from 1.21.2 to 1.21.3

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#89 - Bump pandas from 1.3.3 to 1.3.4

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#88 - Bump click from 8.0.2 to 8.0.3

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#87 - Bed format output needed

Issue - State: closed - Opened by freeedog about 3 years ago - 1 comment

#86 - Can ribotricer infer translation start position?

Issue - State: closed - Opened by freeedog about 3 years ago - 1 comment

#85 - Bump click from 8.0.1 to 8.0.2

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#84 - About ORF nucleotide sequence

Issue - State: closed - Opened by lbwfff about 3 years ago - 1 comment

#83 - Bump pysam from 0.16.0.1 to 0.17.0

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#82 - Bump tqdm from 4.62.2 to 4.62.3

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#81 - Bump pandas from 1.3.2 to 1.3.3

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies