jtlovell GENESPACE issues

jtlovell / GENESPACE

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Load previously generated genespace files instead of re-running everything?

#175 Snodgras closed 7 hours ago
2
Consistent error: if (is.na(gsParam$synteny$hogs)) { : argument is of length zero

#174 Toffeeladd opened 1 week ago
5
OrthoFinder check fails with version 3.0.1b1

#173 odethier-ulb opened 1 week ago
0
GENESPACE can't find the validation path for orthofinder

#172 Luxet closed 1 week ago
5
Error in step 8 of run_genespace()

#171 melop opened 1 month ago
7
"result would exceed 2^31-1 bytes"

#170 CEPHAS-01 opened 1 month ago
9
Error in step 7 of run_genespace

#169 brennandmcdonald closed 1 month ago
0
Update installation instructions to place Bioconductor installs before GENESPACE

#168 jnmaloof opened 2 months ago
0
Add an option to increase number of threads per `diamond` run

#167 taprs opened 2 months ago
1
syntenic block membership

#166 c-m-gibbs opened 2 months ago
3
Running OrthoFinder and MCScanX Outside of GENESPACE

#165 jessiepelosi closed 3 months ago
2
Loss of orthogroups after query_pangenes function?

#164 FSU-pjtb closed 4 months ago
1
HOG path not getting set?

#163 hyphaltip closed 4 months ago
3
Step 4 synteny error

#162 Hannah1746 opened 4 months ago
8
run_orthofinder usage issues

#161 xiaoguizz opened 4 months ago
1
Higlighting small region or gene of interest

#160 dmacguigan opened 5 months ago
5
How to Change Chromosome Shapes or Display Centromeres?

#159 YYsama11 closed 5 months ago
1
Why is it so hard to use GENESPACE?

#158 GurjotSinghSidhu closed 5 months ago
1
BUG when specifying rawOrthofinderDir

#157 dmacguigan closed 5 months ago
1
Error in strsplit(id, ",") at step 2

#156 daniilprigozhin opened 6 months ago
1
Extracting genes used for syntenic blocks

#155 caonetto closed 5 months ago
1
Issue with Specifying Highlighted Regions in highlightBed

#154 YYsama11 closed 6 months ago
2
Error when running run_genespace

#153 topa92 opened 6 months ago
9
Same gene in multiple orthogroups

#152 jacopoM28 opened 7 months ago
0
How are chromosomes labelled by parse_annotations?

#151 plhm closed 5 months ago
1
Using fasta (DNA sequences) and gff file from busco genes

#150 KBeine closed 5 months ago
5
riparian plots are inconsistent

#149 gorliver closed 5 months ago
2
Error in step 3. Combining and annotating the blast files with orthogroup info ...

#148 htorrado opened 7 months ago
11
Step 3. 'Combining and annotating blast files'

#147 plhm closed 5 months ago
3
error in run_genespace

#146 jdobry-lab closed 7 months ago
2
Could not find a valid path to the orthofinder program from R.

#145 celphin closed 9 months ago
1
Synteny / homoeologs in polyploids

#144 tallnuttrbgv closed 5 months ago
3
Parsing error; n unique sequences = 7034, n matched to gff = 0

#143 kcl58759 closed 5 months ago
2
Orthofinder taking very long time

#142 tallnuttrbgv closed 9 months ago
1
clean_windows docs?

#141 tallnuttrbgv closed 5 months ago
1
cannot install dependency 'igraph'

#140 tallnuttrbgv closed 9 months ago
1
Error in if (is.na(gsParam$synteny$hogs)) { : argument is of length zero. when checking orthofinder

#139 cieohsc closed 9 months ago
1
Error when running init_genespace() on phytozome genomes

#138 samseaver closed 5 months ago
5
Display chromosomes with no orthologs in riparian plot

#137 AnthonyPiot91 closed 10 months ago
1
Combining and annotating bed files w/ OGs and tandem array info fails

#136 Jadziaa closed 10 months ago
1
Query Regarding Rerun of OrthoFinder Despite Previous Result Directory Provided

#135 Caoyu819 closed 10 months ago
1
Reading .bed files fails if the .bed file contains more than four columns.

#134 mankiddyman closed 10 months ago
1
Non-syntenic ortholog is not present in pan-genome table

#133 xiaoyezao closed 5 months ago
1
riparian plots based on clean_windows output

#132 akautt closed 10 months ago
1
Plot riparian not the same as dot plots or previous runs of genespace

#131 trm76056 closed 5 months ago
5
Difference between riparian plot plotted in the directory and on console

#130 johannesnicolaus closed 10 months ago
7
ROI riparian plotting error

#129 aamirwkhan06 closed 10 months ago
1
Question about filtering Diamond results

#128 Hannah1746 closed 12 months ago
5
Highlight the gene of interest across the chromosome

#127 HobbitBaba closed 12 months ago
2
Error while parsing

#126 gubrins closed 1 year ago
3