Ecosyste.ms: Issues

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GitHub / BioGenies/tidysq issues and pull requests

#98 - I would like to add x numer of N between concatenated sequences with collapse

Issue - State: open - Opened by ericgonzalezs over 1 year ago - 2 comments
Labels: enhancement

#97 - How do you bite rowwise?

Issue - State: open - Opened by m3hdad over 1 year ago - 2 comments
Labels: discussion

#96 - Fix/incorrect codons

Pull Request - State: closed - Opened by DominikRafacz over 2 years ago
Labels: bug

#95 - translate() uses incorrect codons for DNA to protein conversion

Issue - State: closed - Opened by poppn over 2 years ago - 1 comment
Labels: bug

#94 - bioc check flow bump

Pull Request - State: closed - Opened by DominikRafacz over 2 years ago
Labels: meta

#93 - Add data.frame generics to find_motifs & write_fasta

Pull Request - State: closed - Opened by ErdaradunGaztea over 2 years ago - 1 comment

#92 - Add function to apply `write_fasta` on a data frame

Issue - State: closed - Opened by danlooo over 2 years ago - 5 comments
Labels: enhancement

#91 - Add better check for file existence

Issue - State: open - Opened by ErdaradunGaztea almost 3 years ago
Labels: enhancement

#90 - R session crashes when searching for "^" or "$" motif

Issue - State: open - Opened by DominikRafacz about 3 years ago
Labels: bug

#89 - Interpret [A, C, T, G, N] as dna_ext

Issue - State: open - Opened by ErdaradunGaztea over 3 years ago
Labels: bug, refactor

#88 - CPP_sample_fasta fails when FASTA file is shorter than buffer size

Issue - State: closed - Opened by ErdaradunGaztea over 3 years ago
Labels: bug

#87 - add more test for options with usage of withr

Issue - State: open - Opened by DominikRafacz over 3 years ago

#86 - AMP case study

Issue - State: open - Opened by michbur over 3 years ago

#85 - Refactor specific types of integers (like LenSq) on C++ side

Issue - State: open - Opened by DominikRafacz over 3 years ago
Labels: C++ adventures

#84 - Add more convenience parameters to `sqapply` (like `simplify`)

Issue - State: open - Opened by DominikRafacz over 3 years ago
Labels: enhancement

#83 - Formalize sqibble

Issue - State: open - Opened by DominikRafacz over 3 years ago - 2 comments
Labels: enhancement, discussion, refactor

#82 - Implement has_X as an analogue to remove_X

Issue - State: open - Opened by ErdaradunGaztea over 3 years ago
Labels: enhancement

#81 - Optimize find_motifs() using some specialized string-searching algorythm

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: performance

#80 - Cannot use dplyr::group_by with sq objects

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: bug

#79 - Implement replace_motifs()

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: enhancement

#78 - Include bioseq in comparisons

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: documentation

#77 - Create changelog

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: documentation

#76 - Prettify tidysq options printing

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: refactor

#75 - Implement exporting sq objects (or sqibbles) to LaTeX tables

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: enhancement

#74 - Hide LetterTree, LetterNode and Motif classes from the public

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: enhancement, C++ adventures

#73 - Implement duplicated.sq()

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: enhancement

#72 - Added C++-side tests that cover all 160 cases of packing and unpacking

Pull Request - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: test

#70 - Cover more complicated cases of multichar alphabets packing of strings

Issue - State: closed - Opened by DominikRafacz almost 4 years ago - 1 comment
Labels: enhancement

#69 - Rethink the idea of unpacking NA values in string vectors

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: discussion

#68 - Add tests for all combinations of template parameters for packing and unpacking

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: test

#67 - Add comparison and casting betwenn STD_IT and RCPP_IT objects

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#66 - Use template functions for packing and unpacking instead of explicitly specyfying bit shifts

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: refactor, C++ adventures

#65 - rename LVL_NONE to LVL_SILENT

Issue - State: closed - Opened by ErdaradunGaztea almost 4 years ago
Labels: refactor

#64 - constructing sq with "unt" and multicharacter NA_letter fails

Issue - State: closed - Opened by ErdaradunGaztea almost 4 years ago - 3 comments
Labels: bug

#63 - Add classes to errors

Issue - State: closed - Opened by ErdaradunGaztea almost 4 years ago
Labels: enhancement, good first issue, refactor

#62 - Handle case of codon tables with nontranslatable codons

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#61 - Implement possibility of reading motifs for multiletter alphabets

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#60 - export get_standard_alphabet

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#59 - Rewrite format and print for sq and sq pillar shaft

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: refactor

#58 - Calculate codon tables at compile time

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: enhancement, C++ adventures

#57 - Can we call method of base class directly?

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: C++ adventures

#56 - Add safe mode for atp alphabet when constructing sq and reading_fasta

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#55 - Allow random_sq to use various distributions to generate lengths

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#54 - Make tests for find_motifs more organized

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: test

#53 - Add subclass of OperationVectorToVector that supports ResultWrapper

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#52 - Add paste functionality to sq class

Issue - State: closed - Opened by ErdaradunGaztea almost 4 years ago - 2 comments
Labels: enhancement

#51 - Reorganized typedefs in a clean way and improved Proxy readability

Pull Request - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: refactor

#50 - constructing unt sq with ignore_case = TRUE doesn't ignore case enough

Issue - State: closed - Opened by ErdaradunGaztea almost 4 years ago
Labels: bug

#49 - Set LenSq as an alias for R_xlen_t

Issue - State: closed - Opened by ErdaradunGaztea almost 4 years ago
Labels: refactor

#48 - Stop loading pkg::tibble upon loading tidysq

Issue - State: closed - Opened by ErdaradunGaztea almost 4 years ago - 1 comment
Labels: refactor

#47 - Upgrade random to use seed and random library

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#46 - Add support for relative paths for read and write fasta

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#45 - Implement summary.sq

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: enhancement, good first issue, discussion

#44 - Add safe_mode to import_sq()

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: enhancement

#43 - Implement bite for subsequences

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: enhancement

#42 - Add Sequence::(const_)reverse_iterator

Issue - State: open - Opened by ErdaradunGaztea almost 4 years ago
Labels: enhancement

#41 - Extract common code from FastaSampler and obtain_alphabet

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: refactor

#40 - Replace import_from_R and export_to_R with Rcpp::wrap and Rcpp::as

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#39 - Create generified vector wrapper template

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#38 - Investigate memory copying when using Proxy

Issue - State: open - Opened by DominikRafacz almost 4 years ago

#37 - Use roxygen templates for common documentation parameters

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: documentation, enhancement

#36 - Change parameters type in integration layer to reduce number of casting

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: refactor

#35 - Encode.

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: wontfix

#34 - Recreate sqapply and Operation interface

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#33 - Refactor sq and read_fasta, extract common code and make more compact functions

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: refactor

#32 - Add more convenient aliases for types for interpret_type

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#31 - Add warning handling on C++ side where possible

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#30 - Move internal structures to separate files

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: refactor

#29 - Replace temporary exceptions with enable_if etc.

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: refactor

#28 - Extract common code from Sequence and ProtoSequence, Sq and ProtoSq

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: refactor

#27 - Add more iterators and improve existing

Issue - State: open - Opened by DominikRafacz almost 4 years ago
Labels: enhancement

#26 - Improve Sequence::iterator

Issue - State: open - Opened by DominikRafacz almost 4 years ago - 1 comment
Labels: enhancement, performance

#25 - Move type mappings from TypeMapper to classes responsible for internal types

Issue - State: closed - Opened by DominikRafacz almost 4 years ago
Labels: refactor

#24 - merge

Pull Request - State: closed - Opened by DominikRafacz about 4 years ago - 1 comment

#23 - corrected one more line ending

Pull Request - State: closed - Opened by DominikRafacz about 4 years ago - 1 comment

#22 - Feature vctrs

Pull Request - State: closed - Opened by ErdaradunGaztea over 4 years ago

#21 - Internal generic lengths.sq does not dispatch properly

Issue - State: open - Opened by DominikRafacz over 4 years ago - 4 comments
Labels: bug

#20 - initialized summary() for xxxsq objects (as summary.default now)

Pull Request - State: closed - Opened by ErdaradunGaztea over 4 years ago - 1 comment

#19 - Override "head" for sq so that it prints original length of sq object

Issue - State: closed - Opened by ErdaradunGaztea over 4 years ago - 1 comment
Labels: enhancement, good first issue

#18 - Feature original length

Pull Request - State: closed - Opened by ErdaradunGaztea over 4 years ago

#17 - Choose unified color palette and create logo

Issue - State: open - Opened by DominikRafacz over 4 years ago
Labels: documentation

#16 - Discussion on compare operator `==`

Issue - State: closed - Opened by ErdaradunGaztea over 4 years ago - 1 comment
Labels: discussion

#15 - Add "original_length" attribute to each sequence in sq

Issue - State: closed - Opened by DominikRafacz over 4 years ago
Labels: enhancement

#14 - Add construct_sq_[unt/atp] as a convenience shortcut

Issue - State: closed - Opened by ErdaradunGaztea over 4 years ago - 1 comment
Labels: enhancement, good first issue

#13 - Create flow diagram for construct_sq()

Issue - State: open - Opened by ErdaradunGaztea over 4 years ago
Labels: documentation

#12 - Extract common code between find_motifs and %has% operator

Issue - State: closed - Opened by ErdaradunGaztea over 4 years ago - 1 comment
Labels: enhancement

#11 - Allow using c() on mixed clean/unclean sequences

Issue - State: closed - Opened by ErdaradunGaztea over 4 years ago
Labels: duplicate, enhancement

#10 - anyNA() for sq class

Issue - State: open - Opened by ErdaradunGaztea over 4 years ago
Labels: enhancement

#9 - Add human readable alias and blossum matrix

Issue - State: closed - Opened by michbur about 5 years ago - 2 comments
Labels: enhancement

#8 - More functionality to c() function

Issue - State: closed - Opened by DominikRafacz about 5 years ago - 1 comment
Labels: enhancement, question

#7 - NSE for find_motifs

Issue - State: open - Opened by michbur over 5 years ago
Labels: enhancement

#6 - sessionInfo for tidysq.options

Issue - State: closed - Opened by michbur over 5 years ago - 1 comment

#5 - Synched benchmark branch

Pull Request - State: closed - Opened by michbur over 5 years ago

#4 - Thoughts on PepTools

Issue - State: open - Opened by leonjessen over 5 years ago - 1 comment

#3 - Citations on reproducible computational biology research

Issue - State: closed - Opened by leonjessen over 5 years ago - 1 comment

#2 - Faster implementation of functions

Issue - State: closed - Opened by DominikRafacz over 5 years ago - 1 comment
Labels: enhancement

#1 - Function suggestion: complement()

Issue - State: closed - Opened by leonjessen over 5 years ago - 1 comment