Activity for ViReMa

ViReMa updated /ViReMa_0.29/ViReMa_0.29.zip

ViReMa — Mon, 27 Nov 2023 23:28:02 -0000

ViReMa released /ViReMa_0.29/ViReMa_0.29.zip

ViReMa — Tue, 21 Nov 2023 18:19:02 -0000

ViReMa released /ViReMa_0.28/ViReMa_0.28.zip

ViReMa — Tue, 21 Nov 2023 18:18:06 -0000

Doeun posted a comment on discussion General Discussion

Doeun — Mon, 31 Jul 2023 02:04:25 -0000

I attempted to detect virus integration sites using ViReMa by using the example sample in the source code file. The test run was successful without any errors. However, when I tried using my own samples, the bed file was not generated correctly, so I am reaching out for help. I executed the following command: /home/kde/anaconda3/envs/virema/bin/ViReMa.py \ --Host_Index /home/kde/PROJECTS/VirusIntegrationTools/HBV_C/hg19 \ /home/kde/PROJECTS/VirusIntegrationTools/download/ViReMa/reference/AB033550_padded...

ViReMa released /SupplementaryData_Sotcheff-et-al/SData3_SeV_BED_Files.zip

ViReMa — Mon, 14 Mar 2022 16:34:03 -0000

ViReMa released /SupplementaryData_Sotcheff-et-al/SData4_STIV_BED_Files.zip

ViReMa — Mon, 14 Mar 2022 16:33:03 -0000

ViReMa released /SupplementaryData_Sotcheff-et-al/SData2_HIV_BED_Files.zip

ViReMa — Mon, 14 Mar 2022 16:33:03 -0000

ViReMa released /SupplementaryData_Sotcheff-et-al/SData1_FHVsim_BED_Files.zip

ViReMa — Mon, 14 Mar 2022 16:33:03 -0000

ViReMa released /Simulated_Data_Flock-House-virus/FHVsim_dataset1.fq.gz

ViReMa — Tue, 08 Mar 2022 20:22:42 -0000

ViReMa updated /README.txt

ViReMa — Thu, 03 Jun 2021 19:08:03 -0000

ViReMa released /ViReMa_0.25/ViReMa_0.25.zip

ViReMa — Thu, 03 Jun 2021 19:06:03 -0000

ViReMa updated /README.txt

ViReMa — Mon, 24 May 2021 23:12:03 -0000

ViReMa released /ViReMa_0.24/ViReMa_0.24.zip

ViReMa — Mon, 24 May 2021 23:11:02 -0000

ViReMa updated /ViReMa_0.23/ViReMa_0.23.zip

ViReMa — Tue, 30 Mar 2021 21:17:02 -0000

ViReMa released /ViReMa_0.23/ViReMa_0.23.zip

ViReMa — Tue, 30 Mar 2021 17:50:04 -0000

ViReMa updated /README.txt

ViReMa — Tue, 30 Mar 2021 17:49:02 -0000

Julia Hillung posted a comment on discussion General Discussion

Julia Hillung — Mon, 29 Mar 2021 06:22:06 -0000

Hi, a colleague took over the project and as I can remember it was a problem of versions of programs. You need exactly the versions of programs (bowtie etc..) that are specified for Virema. She created a kind of an extra environment to make the computer acces the correct versions of the programs for running Virema. I hope it helps. If you need I can ask her for more details. cheers, Julia

Nan Jiang posted a comment on discussion General Discussion

Nan Jiang — Fri, 26 Mar 2021 18:41:16 -0000

Hi, I got the same error! have you figured out how to solve it?

Julia Hillung posted a comment on discussion General Discussion

Julia Hillung — Mon, 29 Jun 2020 10:54:54 -0000

Hey, I am very green in bioinformatics, please help! I am trying to run virema with the Test Data and get the error at the end: ('Aligner Directory =', '/Users/evolsysvir10/Desktop/bowtie-0.12.9/') ('Output Directory =', '') Virus Index Found Beginning alignments on Chunk Number 1 10000 reads in input file. 6733 reads remaining to be aligned after first iteration. Traceback (most recent call last): File "ViReMa.py", line 1182, in IterateAlignments('ChunkedReads') File "ViReMa.py", line 1124,...

ViReMa released /ViReMa_0.20/ViReMa_0.20.zip

ViReMa — Tue, 05 May 2020 14:15:05 -0000

ViReMa released /ViReMa_0.20/ConfigViReMa.py

ViReMa — Tue, 05 May 2020 14:15:05 -0000

ViReMa released /ViReMa_0.20/ViReMa.py

ViReMa — Tue, 05 May 2020 14:15:05 -0000

ViReMa released /ViReMa_0.20/LICENSE.txt

ViReMa — Tue, 05 May 2020 14:15:05 -0000

ViReMa released /ViReMa_0.20/Compiler_Module.py

ViReMa — Tue, 05 May 2020 14:15:05 -0000

ViReMa released /Supplementary Scripts/scViReMa_retagger_0.4.py

ViReMa — Wed, 02 Oct 2019 16:40:02 -0000

ViReMa released /Supplementary Scripts/Shannon_Entropy.py

ViReMa — Tue, 07 Aug 2018 13:09:02 -0000

ViReMa released /ViReMa_0.15/ViReMa_0.15.zip

ViReMa — Fri, 27 Jul 2018 15:31:02 -0000

ViReMa released /ViReMa_0.15/ViReMa_0.15.zip

ViReMa — Wed, 25 Jul 2018 15:52:02 -0000

ViReMa released /ViReMa_0.15/ViReMa_0.15.zip

ViReMa — Wed, 25 Jul 2018 14:29:02 -0000

ViReMa released /ViReMa_0.15/ViReMa_0.15.zip

ViReMa — Tue, 24 Jul 2018 22:15:02 -0000

ViReMa released /ViReMa_0.15/ViReMa_0.15.zip

ViReMa — Tue, 24 Jul 2018 21:46:03 -0000

ViReMa released /ViReMa_0.15/Update_notes_ViReMa_0.15.txt

ViReMa — Tue, 24 Jul 2018 19:44:03 -0000

ViReMa released /ViReMa_0.15/ViReMa_0.15.zip

ViReMa — Tue, 24 Jul 2018 19:44:03 -0000

ViReMa released /ViReMa_0.15.zip

ViReMa — Tue, 24 Jul 2018 19:43:03 -0000

ViReMa released /Supplementary Scripts/ViReMa_Count_ORFCount.py

ViReMa — Sat, 09 Jun 2018 14:50:03 -0000

ViReMa released /Supplementary Scripts/ViReMa_Count_mod.py

ViReMa — Sat, 09 Jun 2018 14:48:01 -0000

ViReMa released /Supplementary Scripts/FlagFixer.py

ViReMa — Sat, 09 Jun 2018 14:47:02 -0000

ViReMa released /ViReMa_0.13/ViReMa_0.13.zip

ViReMa — Fri, 01 Jun 2018 18:20:03 -0000

ViReMa released /README.txt

ViReMa — Fri, 01 Jun 2018 18:18:16 -0000

ViReMa released /FHV_Genome_padded.4.ebwt