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737 results • Page 3 of 15
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27
votes
13
replies
6.0k
views
Tool: DEA.R: Command line script for differential expression analysis with R packages (DESeq2/edgeR/limma-voom)
edgeR DESeq2 limma RNA-Seq
updated 10 months ago by 43k • written 7.8 years ago by 47k
9
votes
4
replies
6.0k
views
Tool: BPGA - Bacterial Pan Genome Analysis pipeline
sequence genome comparative-genomics bacteria
updated 11 months ago by 43k • written 8.0 years ago by ▴ 80
5
votes
3
replies
5.9k
views
Tool: CRAVAT: a web tool to annotate and analyze cancer variants
sequencing variant annotation Cancer
updated 2.3 years ago by 43k • written 8.6 years ago by ▴ 1000
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
4
votes
6
replies
5.8k
views
Tool: Fungal genome annotation
genome sequencing
updated 2.4 years ago by 43k • written 9.3 years ago by ▴ 90
10
votes
0
replies
5.8k
views
Tool: Shell utilities for QC of FASTQ/FASTA files (based on perl one-liners)
PERL GNUPLOT FASTA FASTQ FastQC
updated 10 months ago by 43k • written 10.1 years ago by ★ 1.8k
4
votes
3
replies
5.8k
views
Tool: KeggExp: a web server for visualizing KEGG pathways maps when analyzing expression profile data
expression-profile-data pathway-visualization
9 months ago by liux.bio ▴ 360
10
votes
6
replies
5.7k
views
Tool: Shell script to automate trimmomatic for multiple samples
bash shell trimmomatic
updated 11 months ago by 43k • written 5.0 years ago by 5.8k
3
votes
4
replies
5.7k
views
Tool: ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.
ngs.plot NGS-data visualize
updated 14 months ago by 43k • written 10.1 years ago by ▴ 650
53
votes
13
replies
5.7k
views
6 follow
Tool: I made a DNA/gene/bioinformatics-y workshop for 11-16 year olds which people may find useful
school-outreach
updated 16 months ago by 43k • written 9.0 years ago by ★ 4.0k
6
votes
0
replies
5.6k
views
Tool: cnv_facets: somatic Copy Number Variant calling using the facets package
CNV somatic facets cancer
updated 11 months ago by 43k • written 5.4 years ago by 14k
7
votes
5
replies
5.6k
views
Tool: XENA: a new tool for cancer researcher developed by UCSC
ucsc visualization cancer
updated 10 months ago by 43k • written 8.7 years ago by ★ 5.2k
4
votes
5
replies
5.5k
views
Tool: Blob.js - a small javascript library to draw random blobs/shapes
javascript html figure
updated 21 months ago by 43k • written 8.5 years ago by ★ 1.2k
1
vote
2
replies
5.5k
views
Tool: TCGA & METABRIC Breast Cancer Subtype Survival Curve
gene RNA-Seq
updated 11 months ago by 43k • written 6.9 years ago by ▴ 40
9
votes
3
replies
5.4k
views
Tool: Luigi's Monkey Wrench - A small helper library for commandline heavy bioinformatics workflows in Spotify's Luigi workflow tool
workflows luigi python command-line
updated 2.1 years ago by 43k • written 9.2 years ago by ★ 1.3k
2
votes
0
replies
5.4k
views
Tool: NGS Data Analysis Pipeline for Virus Identification
virus
updated 23 months ago by 43k • written 9.1 years ago by ▴ 70
19
votes
2
replies
5.4k
views
Tool: CIViC - Clinical Interpretation of Variants in Cancer
clinical-interpretation civic variant cancer
updated 10 months ago by 43k • written 9.2 years ago by 20k
4
votes
6
replies
5.3k
views
Tool: NtSeq: JavaScript bioinformatics library for nucleotide sequence manipulation and analysis.
alignment JavaScript sequence
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 60
26
votes
4
replies
5.3k
views
Tool: Dgidb - Mining The Druggable Genome
dgidb drug-gene-interaction
updated 10 months ago by 43k • written 10.6 years ago by 20k
7
votes
0
replies
5.3k
views
Tool: Gem: Genome Wide Event Finding And Motif Discovery
motif
updated 10 months ago by 43k • written 11.5 years ago by 6.0k
11
votes
2
replies
5.3k
views
Tool: ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
quality-control quality-assessment ChIP-Seq
updated 10 months ago by 43k • written 10.1 years ago by ★ 2.0k
5
votes
4
replies
5.3k
views
Tool: Contiguator: A Bacterial Genomes Finishing Tool For Structural Insights On Draft Genomes
reference-genome contigs
updated 10 months ago by 43k • written 11.9 years ago by ▴ 770
6
votes
4
replies
5.2k
views
Tool: Sorting bed files with bash sort
bash bed
updated 14 months ago by 43k • written 8.8 years ago by ★ 2.5k
13
votes
6
replies
5.2k
views
Tool: csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
CSV Golang TSV
9 months ago by shenwei356 8.5k
2
votes
6
replies
5.2k
views
Tool: Variantannotation Package (Bioconductor)
snp variant-annotation
updated 10 months ago by 43k • written 11.8 years ago by 20k
56
votes
23
replies
5.2k
views
10 follow
Tool: ASCIIGenome: Text Only Genome Viewer!
terminal genome-browser java ASCIIGenome
updated 11 months ago by 43k • written 7.9 years ago by 14k
7
votes
17
replies
5.1k
views
Tool: SPLiT-Seq Demultiplexing a bash tool for extraction of barcoded single cells
RNA-Seq sequencing
updated 11 months ago by 43k • written 5.7 years ago by ▴ 80
28
votes
17
replies
5.1k
views
7 follow
Tool: PCAtools: everything Principal Components Analysis
eigenvector pca bioconductor R
updated 11 months ago by 43k • written 5.3 years ago by 88k
7
votes
6
replies
5.1k
views
Tool: mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
depth-of-coverage exome WGS
updated 11 months ago by 43k • written 6.3 years ago by 24k
3
votes
0
replies
5.1k
views
Tool: GUI for MrBayes
Phylogenetic-analyses MrBayes Bayesian-inference
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 110
2
votes
0
replies
5.0k
views
Tool: Prodigal: Prokaryotic Dynamic Programming Genefinding Algorithm For Microbial Genomes
annotation
updated 10 months ago by 43k • written 11.7 years ago by 100k
3
votes
5
replies
5.0k
views
Tool: Phevor: Phenotype Driven Variant Ontological Re-Ranking Tool
interpretation prioritization phevor vaast
updated 11 months ago by 43k • written 9.9 years ago by ▴ 30
25
votes
3
replies
5.0k
views
Tool: Quick statistics from the command line
statistics C
updated 17 months ago by 43k • written 8.9 years ago by ★ 2.3k
5
votes
5
replies
5.0k
views
Tool: Mutect: Accurate Identification Of Somatic Point Mutations
mutect
updated 10 months ago by 43k • written 12.1 years ago by 11k
3
votes
15
replies
4.9k
views
Tool: Annocript: completely automated transcriptome annotation pipeline which can also identify putative lncRNAs
annotation RNA-Seq
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 70
2
votes
2
replies
4.9k
views
Tool: Budapest Reference Connectome: a 3D visualization tool to browse connections in the human brain
connectome neuroscience brain
updated 15 months ago by 43k • written 9.0 years ago by ▴ 350
8
votes
0
replies
4.9k
views
Tool: shinyCircos: an R/shiny application for creation of Circos plot interactively
Circos R Shiny Genome
updated 11 months ago by 43k • written 5.8 years ago by ▴ 110
1
vote
2
replies
4.9k
views
Tool: Genetalk - A Platform To Analyse Your Genetic Variant Data And Talk About It
vcf
updated 10 months ago by 43k • written 10.7 years ago by ▴ 130
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
11
votes
12
replies
4.9k
views
Tool: Mapsembler2 targeted micro assembly and visualization of the local assembly graph
minia mapsembler next-gen Assembly
updated 2.1 years ago by 43k • written 9.8 years ago by ▴ 900
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
1
vote
0
replies
4.9k
views
Tool: diffpdb - a simple tool to compare text-content of PDB files
structural-bioinformatics diff pdb-format
updated 22 months ago by 43k • written 9.1 years ago by ▴ 150
13
votes
6
replies
4.9k
views
Tool: GAWN - Genome Annotation Without Nightmares
genome-annotation
updated 11 months ago by 43k • written 6.8 years ago by 11k
18
votes
6
replies
4.9k
views
Tool: R code for ecological data analysis
next-gen R Metagenomics
updated 2.1 years ago by 43k • written 9.3 years ago by ★ 1.8k
6
votes
8
replies
4.9k
views
Tool: Read-based phasing with WhatsHap
phasing
updated 10 months ago by 43k • written 7.4 years ago by ▴ 100
3
votes
5
replies
4.8k
views
Tool: Omicia Opal Research - Variant Annotation and Disease-Gene Prioritization
annotation interpretation vaast
updated 10 months ago by 43k • written 9.9 years ago by ▴ 30
11
votes
1
reply
4.8k
views
Tool: Ideogram.js: a JavaScript library for chromosome visualization
javascript chromosome visualization ideogram
updated 11 months ago by 43k • written 6.2 years ago by ▴ 120
6
votes
6
replies
4.8k
views
Tool: Reading/ Writing FASTA files in Java
FASTA Java
updated 10 months ago by 43k • written 9.4 years ago by • 0
6
votes
2
replies
4.8k
views
Tool: Snpeff - Annotating And Predicting The Effects Of Single Nucleotide Polymorphisms
snp variant-annotation
updated 10 months ago by 43k • written 11.8 years ago by 20k
12
votes
0
replies
4.8k
views
Tool: UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
UMI RNA-Seq single-cell
updated 11 months ago by 43k • written 6.8 years ago by 19k
737 results • Page 3 of 15
Recent Votes
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
The Biostar Herald for Monday, May 20, 2024
Answer: Generating Group/Cluster Lists from fastq files
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Recent Replies
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…
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl by GenoMax 142k
Looks like the samples are from this project: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320483&o=acc_s%3Aa This table has the SR…
Comment: Filter Genome for Specific Sites by Pierre Lindenbaum 161k
> My sites are in an Excel file right now ![enter image description here][1] <!-- was an American educator and academic administrator…
Answer: Filter Genome for Specific Sites by GenoMax 142k
> I have a list of ~1,300 single bp sites Convert your file to plain text [**BED format**][1] (three fields required). Use `bedtools slo…
Comment: How to generate an Upset plot in R to plot the shared variants between cell free by sainavyav22 • 0
It worked, Thank you very much!
Comment: What marks a De-Novo Genome assembly as FAILED? by dthorbur ★ 2.0k
I'm unsure you'll be able to identify whole chromosomes that are not core from illumina reads alone. That might be easier to do with a micr…
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