Limit : all time
all time today this week this month this year
737 results • Page 2 of 15
Sort: replies
Rank Views Votes Replies
21
votes
14
replies
9.5k
views
Tool: trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files
visualization igv ChIP-Seq R bigwigs
updated 11 months ago by 44k • written 3.5 years ago by ★ 3.2k
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 11 months ago by 44k • written 8.0 years ago by ★ 2.5k
4
votes
13
replies
2.8k
views
Tool: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
pathway-analysis visualization Pathview SBGN
updated 11 months ago by 44k • written 3.2 years ago by ▴ 430
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 11 months ago by 44k • written 7.8 years ago by 47k
54
votes
13
replies
10k
views
6 follow
Tool: Bedtools: Analyzing Genomic Features
bedtools
updated 11 months ago by 44k • written 12.1 years ago by 100k
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 44k • written 9.0 years ago by ★ 4.0k
0
votes
13
replies
2.6k
views
Tool: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hitting Time
network driver-gene software
updated 11 months ago by 44k • written 6.8 years ago by ★ 1.1k
9
votes
12
replies
4.6k
views
Tool: fastp v0.9 released: an all-in-one FASTQ preprocessor (QC, adapters, trimming, quality filtering / cutting, splitting output ... )
fastq fastp open-source
updated 11 months ago by 44k • written 6.6 years ago by ★ 2.5k
27
votes
12
replies
11k
views
Tool: Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
QC Trimming Read Trimmer
updated 2.6 years ago by 44k • written 9.9 years ago by 20k
10
votes
12
replies
1.9k
views
Tool: PanDepth, an ultra-fast and efficient genomic tool for coverage calculation
bam paf depth cram coverage
3 months ago by Huiyang ▴ 190
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 44k • written 9.8 years ago by ▴ 900
21
votes
11
replies
11k
views
Tool: Segemehl: A Fast One-Stop-Shop Mapping Tool
mapping next-gen
updated 11 months ago by 44k • written 11.7 years ago by 11k
17
votes
11
replies
11k
views
6 follow
Tool: Pyfaidx: Efficient, "Pythonic" Random Access To Fasta Files Using Samtools-Compatible Indexing
fasta python samtools
updated 11 months ago by 44k • written 10.3 years ago by 10k
7
votes
11
replies
3.2k
views
Tool: Graphical User Interface for creating an automated RNA-Sequencing Pipeline via Kallisto and DESeq2
DESeq2 kallisto RNA-Seq
updated 11 months ago by 44k • written 5.4 years ago by ▴ 60
15
votes
11
replies
8.3k
views
Tool: Arriba: Fast and accurate gene fusion detection from RNA-Seq data
variant-calling RNA-Seq cancer gene-fusion
updated 11 months ago by 44k • written 6.3 years ago by ▴ 150
21
votes
11
replies
2.8k
views
Tool: log / log.bio - keeping track of command line workflows
ac.gt log.bio log
updated 20 months ago by 44k • written 8.7 years ago by 13k
11
votes
10
replies
2.3k
views
Tool: [Crushing the bureaucracy in bioinformatics] Introducing Skymap-JupyterHub: accessing and utilizing reprocessed expression/ allelic read count profil…
SNP RNA-Seq ChIP-Seq
updated 11 months ago by 44k • written 5.8 years ago by ▴ 300
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 44k • written 3.6 years ago by 8.6k
5
votes
10
replies
2.5k
views
Tool: Tools Section Now Enabled
meta biostars
updated 15 months ago by 44k • written 12.1 years ago by 100k
3
votes
10
replies
1.7k
views
Tool: Quick & dirty DNA coordinates in any mac app
sequence alignment
updated 11 months ago by 44k • written 6.2 years ago by ▴ 180
6
votes
10
replies
4.4k
views
Tool: Wham - a structural variant caller and association testing framework
genotype gwas bwa-mem bam structural-variant
updated 2.1 years ago by 44k • written 9.3 years ago by 12k
6
votes
10
replies
4.6k
views
Tool: Giant Virus Finder - discover giant virus sequences in metagenomes
Giant-Virus-Finder
updated 14 months ago by 44k • written 8.2 years ago by ▴ 350
8
votes
10
replies
7.2k
views
7 follow
Tool: Transcription Factor Binding Sites, Motifs and Expression Profiles from ~10200 ChIP-seq and ~20000 RNA-seq samples
ChIP-Seq transcription-factor miRNA lncRNA
updated 13 months ago by 44k • written 7.6 years ago by ▴ 860
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 11 months ago by 44k • written 7.9 years ago by ★ 2.6k
23
votes
10
replies
12k
views
Tool: ggtree: phylogenetic tree visualization and annotation
ggtree phylogeny visualization
updated 11 months ago by 44k • written 7.9 years ago by ★ 2.6k
8
votes
9
replies
9.0k
views
Tool: Lofreq: A Fast And Sensitive Variant-Caller For Inferring Single-Nucleotide Variants From Ngs Data
snp next-gen somatic-variant
updated 11 months ago by 44k • written 11.6 years ago by ★ 2.5k
9
votes
9
replies
4.7k
views
Tool: pyCirclize - Circular visualization in Python
visualization circos matplotlib genome python
updated 9 months ago by • 0 • written 17 months ago by ▴ 150
17
votes
9
replies
6.1k
views
Tool: Pathomx: Metabolic Pathway Visualisation And Analysis
python pathway-visualization
updated 11 months ago by 44k • written 11.1 years ago by ▴ 180
7
votes
9
replies
4.1k
views
Tool: VCF-simplify: a VCF simplification tool.
VCF variants genome
updated 11 months ago by 44k • written 6.1 years ago by ★ 1.6k
46
votes
9
replies
43k
views
7 follow
Tool: Tools to merge overlapping paired-end reads
ngs Assembly fastq
updated 13 months ago by ▴ 50 • written 7.5 years ago by ★ 1.2k
34
votes
9
replies
11k
views
7 follow
Tool: Bwa-Meth: Align And Tabulate Bs-Seq Reads
methylation
updated 11 months ago by 44k • written 10.3 years ago by 24k
4
votes
9
replies
2.7k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by • 0
3
votes
9
replies
3.6k
views
Tool: Download all refseq/genbank bacterial genomes from NCBI
genome sequencing
updated 11 months ago by 44k • written 7.3 years ago by ▴ 10
15
votes
9
replies
3.4k
views
Tool: FlexiDot: highly customizable, ambiguity-aware dotplots
dotplot visualization sequence-analysis
updated 11 months ago by 44k • written 6.0 years ago by ▴ 230
17
votes
9
replies
17k
views
6 follow
Tool: ggrepel: repel overlapping text labels in ggplot2
R visualization
updated 11 months ago by 44k • written 8.4 years ago by ★ 2.3k
16
votes
9
replies
8.7k
views
Tool: Introducing eLabFTW : free open source electronic lab notebook
eln open-source notebook-software
updated 2.4 years ago by 44k • written 9.8 years ago by ▴ 190
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 44k • written 11.1 years ago by ★ 1.7k
12
votes
9
replies
7.8k
views
Tool: gogadget: an R package for go analysis visualization and interpretation
goseq R RNA-Seq gogadget
updated 11 months ago by 44k • written 7.8 years ago by 8.3k
3
votes
8
replies
6.3k
views
Tool: MFEprimer-2.0: A Fast Thermodynamics-Based Program For Checking Pcr Primer Specificity
primer pcr
updated 11 months ago by 44k • written 12.0 years ago by ▴ 170
15
votes
8
replies
2.4k
views
Tool: One Stop Solution for NGS Data Analysis
Predefined Robust NGS Analysis Tool
8.1 years ago by Persistent LABS ▴ 750
5
votes
8
replies
7.1k
views
6 follow
Tool: Converting MUMmer snps file to a real VCF file
VCF mummer SNP
updated 11 months ago by 44k • written 4.8 years ago by ★ 3.6k
8
votes
8
replies
2.9k
views
Tool: DiscoSnp++ 2.1.2 release: now genotypes and creates VCFs
SNP discosnp genotyping indel
updated 24 months ago by 44k • written 9.2 years ago by ▴ 900
12
votes
8
replies
3.2k
views
Tool: BioBit: Global bioinformatics chat
communication
updated 13 months ago by 44k • written 7.9 years ago by ▴ 90
2
votes
8
replies
3.7k
views
Tool: Mirnakey - A Software Pipeline For The Analysis Of Microrna Deep Sequencing Data
mirna
updated 11 months ago by 44k • written 11.8 years ago by 100k
3
votes
8
replies
744
views
Tool: Generate unit-tested, ready-to-run pipelines using natural language prompting
NGS pipeline genomics cloud AI
updated 3 months ago by 44k • written 3 months ago by ▴ 50
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 11 months ago by 44k • written 5.7 years ago by ▴ 580
8
votes
8
replies
3.3k
views
Tool: pyGeno 1.2: Python package for Personalized Genomics and Proteomics
python SNP rna-seq dbSNP ensembl
updated 23 months ago by 44k • written 9.1 years ago by ▴ 220
9
votes
8
replies
3.8k
views
6 follow
Tool: NCBI-SRA File Downloader
NCBI sra sequence
updated 14 months ago by 44k • written 8.7 years ago by ▴ 50
13
votes
8
replies
4.3k
views
Tool: MSigDB for Multiple Organisms in a Tidy Data Format
msigdb pathways R gsea
updated 11 months ago by 44k • written 6.1 years ago by 13k
8
votes
8
replies
4.4k
views
Tool: MetaR: a simple language useful for RNA-Seq data analysis
RNA-Seq R
updated 2.1 years ago by 44k • written 9.4 years ago by ▴ 170
737 results • Page 2 of 15
Recent Votes
C: Classifying normal vs cancer tissues from mutational data
Classifying normal vs cancer tissues from mutational data
Pymol Scripting Help
A: Not sure if pipe from bowtie2 to samtools is working?
Comment: FastQC interpretation - 16S sequencing
Comment: FastQC interpretation - 16S sequencing
Answer: vg autoindex seems stuck after a week of running
Recent Locations • All
Mexico, 1 minute ago
United States, 1 minute ago
Italy, 2 minutes ago
United States, 2 minutes ago
United States, 2 minutes ago
United States, 4 minutes ago
United States, 4 minutes ago
Recent Awards • All
Teacher to Ashutosh Pandey 12k
Popular Question to Wilber0x ▴ 50
Popular Question to pinheirofabiano ▴ 20
Popular Question to andres_arroyo • 0
Popular Question to Tawny ▴ 180
Popular Question to anasjamshed ▴ 120
Student to Rafael Soler ★ 1.2k
Recent Replies
Comment: Trimmomatic running but files containing purged reads are empty by GenoMax 142k
> Why is trimmomatic not removing any reads? It is not mandatory that your data have extraneous/adapter sequence. If no extraneous sequenc…
Comment: FastQC interpretation - 16S sequencing by GenoMax 142k
Since a specific region is being amplified it is expected that many of the library fragments will have identical sequences. Thus the low nu…
Comment: FastQC interpretation - 16S sequencing by Christopher • 0
@genomax Thank you so much for replying. I was quite unsure about the qualities. One more question. There is no problem within nucleotide d…
Comment: FastQC interpretation - 16S sequencing by GenoMax 142k
> My specific question is about the feasibility of per base sequence content analysis and whether I should be concerned about a particular …
Comment: How to get the ratio of allele counts from GATK derived VCF file? by anikcropscience ▴ 230
But I used the same bam files in both freebayes and GATK. Even the overlapping SNPs from both software are giving different estimates in te…
Comment: How to get the ratio of allele counts from GATK derived VCF file? by Pierre Lindenbaum 162k
may be downsampling(?), QC failing reads ?
Comment: How to get the ratio of allele counts from GATK derived VCF file? by anikcropscience ▴ 230
Thank you. However, I extracted the AD for each SNP that gives two numbers separated by a comma. I guess the first one is for reference and…
Answer: How to get the ratio of allele counts from GATK derived VCF file? by Pierre Lindenbaum 162k
> However, I am doing SNP calling using GATK, but there is no such information field for reference and alternate allele counts. it's in …
Comment: samtools write-index by GenoMax 142k
> The index file is older than the data file: alignment.sorted.bam.bai I don't think that warning is going to cause any issues. Not sure w…
Comment: samtools write-index by Pierre Lindenbaum 162k
can you please retry, but add rm -vf alignment.sorted.bam.bai before invoking minimap2. And `-o alignment.sorted.bam` should be enoug…
Answer: from CRAM to fastq by Pierre Lindenbaum 162k
if the CRAM/BAM is paire-end, it **must** be sorted on query name using samtools collate https://x.com/lh3lh3/status/1132756684789768202 …
Comment: from CRAM to fastq by machaalani29 • 0
one of the issues is that I am not very sure how the sequencing was done, but I think it was single end. any suggestions hoot do that?
Comment: from CRAM to fastq by machaalani29 • 0
the option -c is to compress the file
Comment: from CRAM to fastq by GenoMax 142k
Possibly. You appear to have written the data to a single file (in case it was paired-end to begin with). Check to make sure secondary alig…
Comment: converting transcript IDs (Ensembl) to gene symbols in R by GenoMax 142k
https://www.biostars.org/u/18990/ : Please do not delete threads that have received a comment/answer.
Traffic: 2556 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6