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737 results • Page 4 of 15
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Tool: Compi: Application Framework for Portable Computational Pipelines
pipeline workflow-management-system docker
updated 11 months ago by 43k • written 4.6 years ago by ▴ 380
0
votes
0
replies
545
views
Tool: Unicorn Papers - Top ‱ cited papers from PUBMED
citation paper research PUBMED bibliometrics
3.0 years ago by Lukasz Kozlowski • 0
4
votes
7
replies
4.6k
views
6 follow
Tool: MAGERI: a software tool for calling rare variants and detecting circulating tumor DNA from UMI-tagged high-throughput sequencing data
rare-variant resequencing umi ctDNA
updated 3 months ago by • 0 • written 7.0 years ago by 3.5k
1
vote
0
replies
600
views
Tool: Super easy to use free paper retrieval artifact: PyPubMed
python pubmed software
updated 11 months ago by 43k • written 3.0 years ago by ▴ 420
0
votes
0
replies
682
views
Tool: Help solve the cancer puzzle & benefit your research! SimBioSys PhenoScope for integrative multi-modal and multi-omic data analytics
multi-modal multi-omic breast analytics cancer imaging
3.0 years ago by johnpfeiffer • 0
0
votes
0
replies
610
views
Tool: SimBioSys PhenoScope - a cloud-based multi-modal multi-omic data analytics platform for oncology researchers
cloud-based analytic cancer multi-modal multi-omic
3.0 years ago by johnpfeiffer • 0
0
votes
0
replies
702
views
Tool: IPC 2.0: prediction of isoelectric point and pKa dissociation constants
deep-learning isoelectric-point 2D-PAGE pKa
updated 11 months ago by 43k • written 3.0 years ago by • 0
8
votes
6
replies
5.9k
views
Tool: chromoMap- R package for Interactive visualization and Annotation of chromosomes or regions of any living organism.
annotation R genome visualization
updated 11 months ago by 43k • written 5.1 years ago by ▴ 80
0
votes
0
replies
558
views
Tool: Omics Playground Cloud Version
RNA-seq Transcriptomics scRNA-seq Proteomics
3.0 years ago by Axel Martinelli • 0
2
votes
1
reply
887
views
Tool: Complex heatmaps
R heatmap customize
updated 3.0 years ago by 82k • written 3.0 years ago by ★ 27k
13
votes
14
replies
6.2k
views
9 follow
Tool: open-cravat: variant annotation tool
open-cravat
updated 11 months ago by 43k • written 5.4 years ago by ▴ 260
6
votes
3
replies
4.9k
views
Tool: Clustering of short peptide sequences
peptide phage-display clustering
updated 20 months ago by 43k • written 8.6 years ago by ▴ 420
2
votes
1
reply
779
views
Tool: Bioinformatics Programming Package
Package
updated 11 months ago by 43k • written 3.1 years ago by ▴ 10
68
votes
25
replies
16k
views
12 follow
Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq SRA
updated 6 months ago by 142k • written 5.2 years ago by ★ 1.4k
3
votes
1
reply
2.8k
views
Tool: VCF2PopTree: build a phylogenetic tree from a VCF file
VCF2Phylogenetictree
updated 3.1 years ago by ▴ 490 • written 3.2 years ago by ▴ 60
2
votes
0
replies
673
views
Tool: New Tuberculosis in 3D Interactive Viewer
tuberculosis viewer 3D
3.2 years ago by karlynn.noble ▴ 60
2
votes
0
replies
865
views
Tool: New location tracking tool for SARS-CoV-2 variant surveillance
sars-cov-2 variant covid-19
updated 11 months ago by 43k • written 3.2 years ago by ▴ 20
12
votes
5
replies
6.2k
views
Tool: AGAT - Another Gff/Gtf Analysis Toolkit
gff gtf
updated 10 months ago by 43k • written 4.4 years ago by 8.6k
18
votes
39
replies
4.3k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 12 months ago by 43k • written 5.1 years ago by ▴ 50
3
votes
1
reply
1.3k
views
Tool: Introducing Gallia: a Scala library for data manipulation
scala etl json vcf spark
updated 11 months ago by 43k • written 3.3 years ago by ▴ 30
0
votes
0
replies
1.4k
views
Tool: I made QMplot: a python library and tools of generating high-quality manhattan and Q-Q plots for GWAS data
visualization Manhattan-Plot GWAS genome Python
updated 11 months ago by 43k • written 3.2 years ago by • 0
15
votes
2
replies
3.1k
views
Tool: EnhancedVolcano becomes a pseudo-EnhancedMA
enhancedMA enhancedvolcano
updated 11 months ago by 43k • written 3.7 years ago by 88k
4
votes
1
reply
1.3k
views
Tool: rBCS & pyBCS: open-source packages to support interactive visualizations of single-cell data
rna-seq single-cell scrna-seq
updated 11 months ago by 43k • written 3.3 years ago by ▴ 450
0
votes
0
replies
674
views
Tool: MultiLink Analysis: Brain Network Comparison via Sparse Connectivity Analysis
networks neuroscience connectome brain
updated 11 months ago by 43k • written 3.3 years ago by • 0
1
vote
0
replies
685
views
Tool: BiOkeanos - the largest(*) biomedical database catalogue and discovery tool
database catalogue data
updated 11 months ago by 43k • written 3.3 years ago by ▴ 20
0
votes
0
replies
844
views
Tool: Analyze & Visualize Nephele Microbiome Results Using MicrobiomeDB
microbiome sequence
updated 11 months ago by 43k • written 3.3 years ago by ▴ 60
22
votes
20
replies
4.9k
views
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam bam bqsr
updated 11 months ago by 43k • written 5.6 years ago by ▴ 150
7
votes
10
replies
1.5k
views
Tool: SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.
samreadviewer
updated 11 months ago by 43k • written 3.6 years ago by 8.6k
0
votes
0
replies
633
views
Tool: Cytoscape Network analysis
software-error cytoscape
updated 11 months ago by 43k • written 3.3 years ago by • 0
0
votes
3
replies
800
views
Tool: Script: Getting information about SRX experiment ID from NCBI database
next-gen RNA-Seq
updated 15 months ago by 43k • written 3.3 years ago by • 0
0
votes
6
replies
1.5k
views
Tool: Script: Downloading fastq files from ENA database
next-gen-sequencing RNA-Seq
updated 11 months ago by 43k • written 3.3 years ago by • 0
11
votes
2
replies
7.1k
views
Tool: fastp (the ultra-fast all-in-one FASTQ preprocessing tool) v0.18.0 released, 2X faster, with many new features.
fastp QC
updated 11 months ago by 43k • written 5.9 years ago by ★ 2.5k
4
votes
2
replies
1.1k
views
Tool: Alternate the wild type and mutant of SARS-CoV-2 N501Y
SNP
updated 11 months ago by 43k • written 3.4 years ago by ▴ 370
24
votes
26
replies
3.7k
views
Tool: ClinCNV: CNV detection from short reads
variant-calling cna cnv
updated 11 months ago by 43k • written 4.6 years ago by ★ 2.9k
79
votes
86
replies
32k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify storage bbmap pigz compression
updated 11 months ago by 43k • written 7.5 years ago by 20k
34
votes
30
replies
3.0k
views
6 follow
Tool: BioFlows - Container-enabled Bioinformatics pipeline engine
workflow next-gen RNA-Seq pipeline
updated 14 months ago by 43k • written 3.4 years ago by ▴ 90
2
votes
3
replies
1.4k
views
Tool: Filtering BAM files efficiently
BAM genome SAM alignment
updated 11 months ago by 43k • written 3.5 years ago by • 0
2
votes
1
reply
1.2k
views
Tool: Alternate wild type and mutant of SNPs in 3D
Jupyter-Notebook iCn3D SNP 3D-viewer
updated 11 months ago by 43k • written 3.8 years ago by ▴ 370
3
votes
0
replies
889
views
Tool: ChromSCape - A R/Shiny application to analyze single-cell epigenomics data
ChIP-Seq R scChIP-seq scATAC-seq single-cell
updated 11 months ago by 43k • written 3.5 years ago by ▴ 120
2
votes
0
replies
770
views
Tool: driveR - Prioritizing Cancer Driver Genes Using Genomics Data
R driver-gene cancer
updated 11 months ago by 43k • written 3.5 years ago by ★ 1.3k
1
vote
2
replies
1.1k
views
Tool: Graphia: A platform for the graph-based visualisation and analysis of complex data
networks high-dimensional-data transcriptomics
updated 11 months ago by 43k • written 3.6 years ago by ▴ 10
3
votes
0
replies
986
views
Tool: Trimviz, a lightweight QC tool to assess impact of read-trimming and aligner soft-clipping
alignment trimming QC clipping fastq
updated 11 months ago by 43k • written 3.6 years ago by ▴ 140
1
vote
0
replies
961
views
Tool: Introducing WARP: A collection of cloud-optimized workflows for biological data processing and analysis
wdl workflows genomics epigenomics single-cell
updated 11 months ago by 43k • written 3.6 years ago by ★ 1.2k
31
votes
22
replies
13k
views
6 follow
Tool: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
FASTQ SeqKit FASTA
updated 11 months ago by 43k • written 7.6 years ago by 8.5k
2
votes
1
reply
1.1k
views
Tool: Machine learning Python API for ligand-protein binding-affinity prediction
machine-learning binding-affinity R api python
updated 11 months ago by 43k • written 3.6 years ago by ▴ 20
1
vote
1
reply
949
views
Tool: PathogenAR - Structural Biology in Augmented Reality
augmented-reality influenza pathogen
updated 11 months ago by 43k • written 3.9 years ago by ▴ 60
56
votes
52
replies
50k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 11 months ago by 43k • written 9.8 years ago by 7.5k
0
votes
3
replies
1.5k
views
Tool: New data transformation tool for Windows and Mac
data-wrangling software data-munging
updated 11 months ago by 43k • written 3.8 years ago by • 0
4
votes
1
reply
3.9k
views
Tool: kg: query kegg from the command line
kegg kg
updated 11 months ago by 43k • written 8.9 years ago by ▴ 960
4
votes
0
replies
918
views
Tool: Fix Prokka fragmented gene annotations - Long read assembly
fragmented-gene-annotation Prokka
updated 11 months ago by 43k • written 3.6 years ago by 8.6k
737 results • Page 4 of 15
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Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
A: Bcftools merge taking too much time and producing large file
Answer: Kraken2 database
A: Why gene expression data should be log2 transformed?
Answer: Filter Genome for Specific Sites
Answer: Filter Genome for Specific Sites
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
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Recent Replies
Comment: Add stats to the plot by Ghada • 0
Thanks. Unfortunately, the code did not work :( 101010 > data4_test <- data4.ts %>% + ungroup() %>% + t.test(value ~ Condition) %>% + …
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Hello I have a quick question, I did as you said , and further added the traits, found the correlation among the modules and the traits us…
Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial) by ojaswinipandey • 0
Thank you so much Dave.
Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial) by Dave Carlson ★ 1.7k
The y axis represents the proportion of the total variance explained by each principal component. It's negative because the value (between…
Comment: Error in using BioSampleParser tool: subscript out of bounds by marco.barr ▴ 130
Hi Mohamed, I also thought the same thing but we run the risk of inserting other errors perhaps by modifying the function. I tried but I ha…
Comment: Trimming tool by Ram 43k
Please do a few simple Google searches before asking others for help.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award by Ram 43k
This post does not fit the theme of this forum.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award by Ram 43k
Hi, Congratulations but this is not LinkedIn, we are not a place to showcase your professional accomplishments. This does not fall under t…
Comment: Kraken2 Custom Database non-deterministic results by GenoMax 142k
Many (most?) programs related to NGS data analysis produce non-deterministic output (unless they explicitly offer an option to produce dete…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl by GenoMax 142k
For those samples it appears that raw data was not submitted. Just an assembly. $ esearch -db biosample -query SAMN08009548 | elink -…
Comment: How can I calculate the OS of each patient? by Pedro • 0
**I have already tried this code. listSamples with HNSC cancer and smokers. I need at least one supporting material to find out the survi…
Comment: Filter Genome for Specific Sites by Anita • 0
Great, thank you!
Comment: Filter Genome for Specific Sites by Anita • 0
This is unhelpful and doesn't answer my question.
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl by Harshita • 0
It seems that the authors in this paper have used paired-end sequences only for their analysis, and for that, they would also have used the…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl by Harshita • 0
Thank you so much for helping me out in this! I have used most of the sequences that are found in this table. But, some samples like the…
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