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518 results • Page 2 of 11
Sort: Views
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19
votes
14
replies
8.2k
views
7 follow
Tool: AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
PolyG Quality-Control Filtering Fastq AfterQC
updated 10 months ago by 43k • written 8.0 years ago by ★ 2.5k
25
votes
19
replies
8.2k
views
10 follow
Tool: pathfindR - Enrichment Analysis using Active Subnetworks
subnetwork R pathway-enrichment
updated 10 months ago by 43k • written 6.2 years ago by ★ 1.3k
4
votes
0
replies
8.2k
views
Tool: Snprelate: A Toolset For Relatedness And Principal Component Analysis Of Snp Data
parallel pca r
updated 10 months ago by 43k • written 11.2 years ago by 11k
19
votes
5
replies
8.0k
views
Tool: deepTools: user-friendly tools for the normalization and visualization of deep-sequencing data
Visualisation RNA-Seq QC ChIP-Seq
updated 10 months ago by 43k • written 10.0 years ago by ▴ 670
3
votes
1
reply
8.0k
views
Tool: New ultrafast interval tree implementation for Python: kerneltree
Interval-tree Python
updated 10 months ago by 43k • written 6.0 years ago by ▴ 960
14
votes
10
replies
7.9k
views
Tool: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
ReactomePA R Visualization Pathway Bioconductor
updated 10 months ago by 43k • written 7.8 years ago by ★ 2.6k
0
votes
2
replies
7.9k
views
Tool: The script to install the required packages for gene expression analysis using DESeq2 for downstream analysis and visualization
R RNAseq installation DESeq2
9 months ago by Aditya naman • 0
12
votes
9
replies
7.8k
views
Tool: gogadget: an R package for go analysis visualization and interpretation
goseq R RNA-Seq gogadget
updated 10 months ago by 43k • written 7.8 years ago by 8.3k
19
votes
4
replies
7.7k
views
Tool: NanoPack: Scripts for long read sequencing data processing and analysis: NanoPlot, NanoFilt, NanoStat, NanoLyse, NanoComp
pacbio long-reads oxford-nanopore
updated 10 months ago by 43k • written 6.6 years ago by 47k
16
votes
16
replies
7.7k
views
6 follow
Tool: Oncofuse: Prediction Of Driver Gene Fusions From Ngs Data
annotation fusion rna-seq ngs
updated 10 months ago by 43k • written 10.7 years ago by 3.5k
3
votes
1
reply
7.5k
views
Tool: Weeder 2.0 - motif discovery tool updated
motif-discovery chip-seq weeder
updated 10 months ago by 43k • written 9.6 years ago by 6.0k
10
votes
1
reply
7.5k
views
Tool: Comb-P: Combining Spatially Correlated P-Values
methylation
updated 10 months ago by 43k • written 11.6 years ago by 24k
13
votes
2
replies
7.4k
views
Tool: Software For Detecting Differential Abundance In Meta-Genomic Samples
metagenomics
updated 10 months ago by 43k • written 11.6 years ago by 100k
4
votes
3
replies
7.3k
views
Tool: Deindexer - A Standalone Demultiplexing Tool For Illumina Platform
illumina
updated 10 months ago by 43k • written 11.3 years ago by ▴ 110
20
votes
23
replies
7.2k
views
6 follow
Tool: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
easeq Windows Visualization ChIP-Seq
updated 10 months ago by 43k • written 8.1 years ago by ▴ 460
15
votes
6
replies
7.2k
views
Tool: Sambamba: High Performance Alternative For Samtools And Picard For Indexing, Sorting And Merging Bam Files
sambamba bam samtools
updated 10 months ago by 43k • written 10.6 years ago by ★ 5.3k
6
votes
3
replies
7.1k
views
Tool: BioCircos.R: create shiny-friendly interactive multi-track circular plots in R
circos R htmlwidgets shiny
updated 10 months ago by 43k • written 6.4 years ago by ▴ 60
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 10 months ago by 43k • written 5.9 years ago by ★ 2.5k
5
votes
8
replies
7.0k
views
6 follow
Tool: Converting MUMmer snps file to a real VCF file
VCF mummer SNP
updated 10 months ago by 43k • written 4.7 years ago by ★ 3.6k
9
votes
1
reply
7.0k
views
Tool: Rsem: Accurate Transcript Quantification From Rna-Seq Data With Or Without A Reference Genome
rna-seq RSEM
updated 10 months ago by 43k • written 11.6 years ago by 100k
1
vote
4
replies
6.8k
views
Tool: Jellyfish - Fast, Parallel K-Mer Counting For Dna
jellyfish
updated 10 months ago by 43k • written 12.0 years ago by 100k
5
votes
1
reply
6.6k
views
Tool: Trim Adapters Of Paired-End Reads (Fastq)
paired-end adaptor-trimming ngs
updated 10 months ago by 43k • written 11.2 years ago by 11k
3
votes
2
replies
6.6k
views
Tool: Ancestry: AngularJS module with interactive lineage chart components based on D3.js
visualization
updated 10 months ago by 43k • written 7.8 years ago by ▴ 90
22
votes
8
replies
6.6k
views
Tool: BioTuring Browser: Making single-cell sequencing data in published studies really accessible!
scRNA-Seq single-cell
updated 10 months ago by 43k • written 5.6 years ago by ▴ 580
13
votes
1
reply
6.5k
views
Tool: clusterProfiler: an R package for comparing biological themes among gene clusters
GO clusterProfiler KEGG R GSEA
updated 10 months ago by 43k • written 7.8 years ago by ★ 2.6k
7
votes
6
replies
6.5k
views
Tool: PlantTFDB and PlantRegMap: Plant Transcription Factor Database and Plant Regulation Data and Analysis Platform
transcriptional-regulation enrichment binding-site
updated 10 months ago by 43k • written 7.6 years ago by ▴ 80
3
votes
8
replies
6.3k
views
Tool: MFEprimer-2.0: A Fast Thermodynamics-Based Program For Checking Pcr Primer Specificity
primer pcr
updated 10 months ago by 43k • written 11.9 years ago by ▴ 170
10
votes
3
replies
6.3k
views
Tool: GenVisR: Genomic Visualizations in R
visualization genomic RNA-Seq genvisr
updated 10 months ago by 43k • written 7.9 years ago by 20k
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
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
2
votes
5
replies
6.1k
views
Tool: umitools - working with UMI incorporated data
UMI sequencing
updated 10 months ago by 43k • written 9.9 years ago by ▴ 70
17
votes
9
replies
6.1k
views
Tool: Pathomx: Metabolic Pathway Visualisation And Analysis
python pathway-visualization
updated 10 months ago by 43k • written 11.1 years ago by ▴ 180
19
votes
9
replies
6.1k
views
Tool: Rlsim, A Package For Simulating Rna-Seq Library Preparation With Parameter Estimation
simulation rna-seq pcr illumina
updated 11 months ago by 43k • written 11.1 years ago by ★ 1.7k
18
votes
2
replies
6.0k
views
Tool: vcfanno quickly annotate a vcf with other VCFs, BEDs, BAMs
VCF variant-annotation
updated 10 months ago by 43k • written 8.9 years ago by 24k
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
5.9k
views
Tool: BPGA - Bacterial Pan Genome Analysis pipeline
sequence genome comparative-genomics bacteria
updated 10 months ago by 43k • written 8.0 years ago by ▴ 80
8
votes
6
replies
5.8k
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
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 10 months ago by 43k • written 5.0 years ago by 5.8k
6
votes
0
replies
5.6k
views
Tool: cnv_facets: somatic Copy Number Variant calling using the facets package
CNV somatic facets cancer
updated 10 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
1
vote
2
replies
5.4k
views
Tool: TCGA & METABRIC Breast Cancer Subtype Survival Curve
gene RNA-Seq
updated 10 months ago by 43k • written 6.9 years ago by ▴ 40
19
votes
2
replies
5.3k
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
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
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
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
2
votes
6
replies
5.2k
views
Tool: Variantannotation Package (Bioconductor)
snp variant-annotation
updated 10 months ago by 43k • written 11.7 years ago by 20k
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
518 results • Page 2 of 11
Recent Votes
Answer: What does the 'E%' represent in BUSCO results?
Answer: Combine Two Affymetrix Datasets With Same Platform
Comment: Kraken2 database
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
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Recent Replies
Answer: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
Ah your edit solved this. 50 BUSCOs contain internal stop codons, indicating they might be erroneous gene models, or the genes themselves a…
Answer: MGLTools does not work in windows 11 by Ashfaq • 0
In my case, I did not see iGPU. There is only one option, Intel UHD Graphics. What I need to do?
Comment: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
funny enough i tried the same thing (i've used BUSCO heaps times but never saw the E:! even the manual lists 'C:89.0%[S:85.8%,D:3.2%],F:6.9…
Comment: What does the 'E%' represent in BUSCO results? by GenoMax 142k
According to ChatGPT: In BUSCO, the "E" category represents "End" or "Endof" gene fragments. These are orthologous groups for which the ge…
Comment: Help with IGV abbreviation by GeneC • 0
Thank you for the link and details
Comment: Help with IGV abbreviation by GeneC • 0
Thank you very much for helping with the details.
Comment: How does gene length effect the number of reads mapped by Chen • 0
thank you :)
Answer: Filtering based on alternate allelic balance by Arton • 0
I found the answer when using bcftools. Is there is a way to do this with FilterVcf? bcftools filter --include '(FMT/AD[0:1])/(FMT/A…
Comment: Help with IGV abbreviation by GenoMax 142k
Those are SAM format fields. Check section 1.4 here: https://samtools.github.io/hts-specs/SAMv1.pdf > 1:2114:12111:13792 That is part of …
Answer: Help with IGV abbreviation by Mathew ▴ 130
Hi, here is a breakdown of each part that you asked about: **flag 99**: This indicates various properties of the read alignment. In this c…
Comment: Kraken2 database by Mathew ▴ 130
I don't see any databases with just pathogenic bacteria genomes from just a quick search, I would imagine that using the Standard-16 databa…
Comment: Galaxy StringTie error by Mathew ▴ 130
I am not sure if this is true for Galaxy, but when I code in Python, SyntaxWarning: invalid escape sequence '' occurs when you want to add …
Comment: Can diamond prepdb be used to make a taxonomically aware database? by GenoMax 142k
Should be possible: https://www.biostars.org/p/430366/ Are you using an older version of `diamond`? Latest versions of `diamond` can use N…
Comment: SNPEff database building error by Fungal genetics • 0
Hi, Below SNPEff database building error I am getting. "FATAL ERROR: Most Exons do not have sequences!" The headers are correct and sam…
Comment: Extracting named fasta sequences according to list with Biopython by Rubayetul • 0
the last line of SeqIO.write(record.....'fasta') in a for loop will input the the last record into new fasta file and it will only contain …
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