jbloomlab/dms_tools2 issues and pull requests

#72 - PIP Error when Installing dms_tools2

Issue - State: open - Opened by kevinmyers 7 months ago - 5 comments

#71 - Unable to install DMS in conda env or Run Digens 2018 example Notebook

Issue - State: open - Opened by karenHDT 9 months ago - 2 comments

#70 - Issues Installing dms_tools2

Issue - State: open - Opened by sz1999 over 1 year ago - 1 comment

#69 - issues installing dms_tools2

Issue - State: open - Opened by dylanc-14 about 2 years ago - 2 comments

#68 - Not possible to install

Issue - State: open - Opened by anandasm about 2 years ago - 2 comments

#67 - fixed bug parsing version of fastq-dump >= 3.0.0

Pull Request - State: closed - Opened by couteiral about 2 years ago - 1 comment

#66 - fixed bug parsing version of fastq-dump >= 3.0.0

Pull Request - State: closed - Opened by couteiral about 2 years ago

#65 - Compiling errors for newer Mac OS (Xcode commandline tools)

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

#64 - weblogo plot image artifacts.

Issue - State: closed - Opened by adalisan almost 3 years ago - 5 comments

#63 - One sample and only 1 barcode (single-end run)?

Issue - State: closed - Opened by RicardoBiol almost 3 years ago - 1 comment

#62 - using regex for version parsing

Pull Request - State: closed - Opened by FlyinTeller almost 3 years ago

#61 - Issue with fastq-dump version string

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

#60 - Problem with error conrtols

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

#59 - unconfirmed bug in python code

Issue - State: open - Opened by adalisan about 3 years ago - 1 comment

#58 - _cutils.c asks for Python developer header files not present by default

Issue - State: closed - Opened by JiaGengChang about 3 years ago

#57 - pin `numpy` < 1.20

Pull Request - State: closed - Opened by jbloom over 3 years ago

#56 - pin `pystan` to < 3

Pull Request - State: closed - Opened by jbloom over 3 years ago

#55 - `fastqFromSRA` works with newer `fastq-dump`

Pull Request - State: closed - Opened by jbloom over 3 years ago

#54 - Analysis with single-Read data

Issue - State: closed - Opened by euphowayne78 almost 4 years ago - 2 comments

#53 - no need for max `biopython` version

Pull Request - State: closed - Opened by jbloom about 4 years ago

#52 - pin `pandas`, `biopython`, and `matplotlib` to max versions to avoid errors

Pull Request - State: closed - Opened by jbloom about 4 years ago

#51 - Update path to biopython IUPAC module in init

Pull Request - State: closed - Opened by nguyenvanessa about 4 years ago

#50 - init.py file points to missing biopython module

Issue - State: closed - Opened by nguyenvanessa about 4 years ago - 3 comments

#49 - Initial package setup results in dependency issues?

Issue - State: closed - Opened by jmath97 over 4 years ago - 2 comments

#48 - Question about alignment

Issue - State: closed - Opened by tos2014 over 4 years ago - 6 comments

#47 - `dms2_batch_bcsubamp` handles `bclen` of 0

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

#46 - Question about arguments (--bclen2 10 --bclen 0)

Issue - State: closed - Opened by tos2014 over 4 years ago - 8 comments

#45 - Errors running examples

Issue - State: closed - Opened by lconde-ucl over 4 years ago - 2 comments

#44 - fix version error with `fastq-dump`

Pull Request - State: closed - Opened by jbloom almost 5 years ago

#43 - fastqFromSRA error

Issue - State: closed - Opened by adingens almost 5 years ago - 1 comment

#42 - Added `--bcinfo_csv` argument to `dms2_bcsubamp`

Pull Request - State: closed - Opened by khdcrawford about 5 years ago - 1 comment

#41 - Output `bcInfo` in `.csv`

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

#40 - added pseudocount to raw codon counts in `syn_selection_by_codon`

Pull Request - State: closed - Opened by fwelsh about 5 years ago - 4 comments

#39 - track codoncounts / prefs for Doud2016

Pull Request - State: closed - Opened by jbloom about 5 years ago

#38 - Updated CHANGELOG for `syn_selection`

Pull Request - State: closed - Opened by jbloom about 5 years ago

#37 - Updated to version 2.6.2

Pull Request - State: closed - Opened by jbloom about 5 years ago

#36 - Updated to version 2.6.2

Pull Request - State: closed - Opened by fwelsh about 5 years ago - 1 comment

#35 - Updated for addition of syn_selection module

Pull Request - State: closed - Opened by fwelsh about 5 years ago - 1 comment

#34 - adding syn_selection_by_codon module

Pull Request - State: closed - Opened by fwelsh about 5 years ago - 1 comment

#33 - added `utils.codon_to_nt_counts`

Pull Request - State: closed - Opened by jbloom about 5 years ago

#32 - Add chartype = nucleotide to dms2_bcsubamp

Issue - State: closed - Opened by adingens about 5 years ago - 2 comments

#31 - make compatible with python 3.7

Pull Request - State: closed - Opened by jbloom about 5 years ago

#30 - removed dependency on `HTSeq`

Pull Request - State: closed - Opened by jbloom about 5 years ago