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smith-chem-wisc
/
Spritz
Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
https://smith-chem-wisc.github.io/Spritz/
MIT License
7
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11
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user feedback and recalibration indexing
#142
acesnik
closed
5 years ago
0
Choice of indel finder, enabling exome/wgs sequencing analysis, workers for parallelizing variant calling
#141
acesnik
closed
5 years ago
0
Choose which indels to use (if any), create protein XML from ensembl reference directly
#140
acesnik
closed
5 years ago
0
more messagebox interactions
#139
acesnik
closed
5 years ago
0
Show error messages from the CMD run
#138
acesnik
closed
5 years ago
0
Jeko Fixes
#137
acesnik
closed
5 years ago
1
fix vcf selection
#136
acesnik
closed
5 years ago
0
Confirm that use of BLAST's `-max_target_seqs` is intentional
#135
armish
closed
2 years ago
4
testfix
#134
acesnik
closed
5 years ago
0
Possible bug: not using ensembl-referenced dbsnp VCF for variant calling
#133
acesnik
closed
5 years ago
1
Fixsratoolkitcrash
#132
acesnik
closed
5 years ago
0
Warn user that "MatePair" must be specified before running sample
#131
acesnik
opened
5 years ago
0
dont notify when done.
#130
acesnik
closed
5 years ago
0
updated mzLib, output fasta with applied variants, fix errors with spaces
#129
acesnik
closed
5 years ago
0
Ability to get Ensemble sequences w/ uniprot mods etc without fastq file
#128
leahvschaffer
closed
5 years ago
1
Show default file selections if they already exist in Workflow window
#127
acesnik
closed
4 years ago
0
fasterq-dump
#126
acesnik
closed
5 years ago
0
Escape spaces
#125
acesnik
closed
5 years ago
0
check installation in gui; handle spaces
#124
acesnik
closed
5 years ago
0
Making Spritz cross-platform to cater to the genomics community
#123
acesnik
closed
4 years ago
3
MessageBox that says when installation is finished
#122
acesnik
closed
5 years ago
1
Don't display the main GUI upon closing the installation window if Ubuntu bash isn't installed, yet
#121
acesnik
closed
5 years ago
1
images
#120
acesnik
closed
6 years ago
1
Display FASTQ files in DataGridView of GUI after downloading an SRA
#119
acesnik
closed
4 years ago
2
Use snpEff.config to guide which genomes we download
#118
acesnik
closed
4 years ago
3
scalpel installation check
#117
acesnik
closed
6 years ago
0
Fire up EXE instead of trying to run it like a DLL
#116
acesnik
closed
6 years ago
0
look for local ubuntu
#115
acesnik
closed
6 years ago
0
setup kinks
#114
acesnik
closed
6 years ago
0
Spritz GUI working
#113
acesnik
closed
6 years ago
0
SnpEff speedy option doesn't work so well
#112
acesnik
closed
6 years ago
0
Make method to test tool setup
#111
acesnik
closed
6 years ago
0
Update GUI
#110
lonelu
closed
6 years ago
1
Version issues with (bio)conda if we use it in the future... Nonissues if we use Docker
#109
acesnik
closed
4 years ago
1
Set default thread count to n-1 unless only 1 is available
#108
acesnik
closed
5 years ago
0
swap .count() for .length in Hisat2 Wrapper
#107
rmmiller22
closed
6 years ago
0
Hisat2
#106
rmmiller22
closed
6 years ago
0
Full protein variant annotation now checks out
#105
acesnik
closed
6 years ago
0
Investigate error where getVariant().line is null in SnpEff for variants that aren't even in the VCF
#104
acesnik
closed
6 years ago
1
Filtering VCF (manually, with vcftools) causes ProteinXML not to output sequence variations...
#103
acesnik
closed
5 years ago
1
Moved tests to proteogenomics; allow transcript quantification flow on compressed files
#102
acesnik
closed
6 years ago
0
Make quantification workflow work with gunzipped fastqs
#101
acesnik
closed
6 years ago
1
Use avg read length for stringtie merge range
#100
acesnik
closed
5 years ago
0
Implemented GTF writing and snpeff building with new GTFs
#99
acesnik
closed
6 years ago
0
Differentiating genome and protein fastas in GUI loads
#98
acesnik
closed
4 years ago
0
GUI by command
#97
lonelu
closed
6 years ago
0
Expand CDS determination
#96
acesnik
closed
5 years ago
0
Revamp lncRNAdiscovery to use stringtie models directly and ditch RSEM...
#95
acesnik
closed
6 years ago
0
Bug fixes in STARFusion and stringtie workflows
#94
acesnik
closed
6 years ago
0
Couple more bug fixes
#93
acesnik
closed
6 years ago
0
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