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733 results • Page 2 of 15
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22
votes
20
replies
4.8k
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 10 months ago by 43k • written 5.5 years ago by ▴ 150
22
votes
17
replies
4.0k
views
Tool: epic: new ChIP-Seq caller based on the SICER algorithm
ChIP-Seq
updated 10 months ago by 43k • written 8.1 years ago by ▴ 960
21
votes
11
replies
2.8k
views
Tool: log / log.bio - keeping track of command line workflows
ac.gt log.bio log
updated 19 months ago by 43k • written 8.7 years ago by 13k
21
votes
11
replies
11k
views
Tool: Segemehl: A Fast One-Stop-Shop Mapping Tool
mapping next-gen
updated 10 months ago by 43k • written 11.6 years ago by 11k
21
votes
14
replies
9.4k
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 10 months ago by 43k • written 3.4 years ago by ★ 3.2k
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
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
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
19
votes
5
replies
8.9k
views
Tool: Automatic IGV snapshot script
ChIP-Seq IGV
updated 13 months ago by 43k • written 7.2 years ago by ★ 3.5k
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
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 10 months ago by 43k • written 11.1 years ago by ★ 1.7k
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
18
votes
6
replies
4.8k
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
18
votes
21
replies
4.4k
views
Tool: uQ - small binary FASTQ
Compression FASTQ
updated 10 months ago by 43k • written 7.2 years ago by 13k
18
votes
1
reply
3.5k
views
Tool: Human NGS Cancer Data for tool development, algorithm benchmarking, teaching, pipeline evaluation, etc.
WGS Benchmarking Cancer-Data
updated 18 months ago by 43k • written 8.8 years ago by 19k
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 8.8 years ago by 24k
18
votes
39
replies
4.3k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 11 months ago by 43k • written 5.1 years ago by ▴ 50
18
votes
22
replies
4.6k
views
Tool: FAST: FAST Analysis of Sequences Toolbox
NCBI-Taxonomy pipeline multiFASTA BioPerl
updated 22 months ago by 43k • written 9.1 years ago by ▴ 70
18
votes
30
replies
10k
views
6 follow
Tool: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
Illumina BBMap filterbytile
updated 10 months ago by 43k • written 7.4 years ago by 20k
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 10 months ago by 43k • written 10.2 years ago by 10k
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
17
votes
9
replies
17k
views
6 follow
Tool: ggrepel: repel overlapping text labels in ggplot2
R visualization
updated 10 months ago by 43k • written 8.3 years ago by ★ 2.3k
17
votes
25
replies
2.4k
views
Tool: Platform for Bioinformatics Students, Scholars and Scientists
sequence genome
updated 10 months ago by 43k • written 8.2 years ago by ▴ 50
16
votes
16
replies
7.6k
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
16
votes
3
replies
11k
views
Tool: Vcflib Documentation
vcf
updated 10 months ago by 43k • written 11.1 years ago by ★ 2.4k
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 43k • written 9.7 years ago by ▴ 190
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 10 months ago by 43k • written 6.2 years ago by ▴ 150
15
votes
9
replies
3.3k
views
Tool: FlexiDot: highly customizable, ambiguity-aware dotplots
dotplot visualization sequence-analysis
updated 10 months ago by 43k • written 6.0 years ago by ▴ 230
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
15
votes
8
replies
2.4k
views
Tool: One Stop Solution for NGS Data Analysis
Predefined Robust NGS Analysis Tool
8.0 years ago by Persistent LABS ▴ 750
15
votes
19
replies
8.7k
views
6 follow
Tool: Gemini: Integrative Exploration Of Genetic Variation And Genome Annotations
vcf database genome variation
updated 10 months ago by 43k • written 11.0 years ago by 12k
15
votes
2
replies
3.1k
views
Tool: EnhancedVolcano becomes a pseudo-EnhancedMA
enhancedMA enhancedvolcano
updated 10 months ago by 43k • written 3.7 years ago by 87k
14
votes
3
replies
4.1k
views
Tool: Bedops V2.2 Released
bed
updated 10 months ago by 43k • written 11.0 years ago by 35k
14
votes
4
replies
4.5k
views
Tool: Seq_File: C Library For Reading Multiple Bioinformatics Sequence File Formats
fasta fastq bam sam
updated 10 months ago by 43k • written 11.4 years ago by 22k
14
votes
10
replies
7.8k
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
14
votes
4
replies
4.8k
views
Tool: Revolution (?) in CNA detection using exome/targeted sequencing
copy-number-alteration next-gen
updated 10 months ago by 43k • written 9.0 years ago by ★ 7.8k
13
votes
6
replies
5.1k
views
Tool: csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
CSV Golang TSV
8 months ago by shenwei356 8.5k
13
votes
6
replies
4.8k
views
Tool: GAWN - Genome Annotation Without Nightmares
genome-annotation
updated 10 months ago by 43k • written 6.8 years ago by 11k
13
votes
6
replies
3.0k
views
Tool: Open source bioinformatics tools: Blaster, Primer Factory, Labtools
primer blast alignment bowtie
updated 2.4 years ago by 43k • written 9.3 years ago by ▴ 110
13
votes
1
reply
3.7k
views
Tool: Script to compute the effective genome size: epic-effective
ChIP-Seq
updated 10 months ago by 43k • written 8.1 years ago by ▴ 960
13
votes
14
replies
6.1k
views
9 follow
Tool: open-cravat: variant annotation tool
open-cravat
updated 10 months ago by 43k • written 5.4 years ago by ▴ 260
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
13
votes
7
replies
4.2k
views
Tool: I-PV: a CIRCOS module for interactive protein sequence visualization
interactive javascript circos sequence
updated 20 months ago by 43k • written 8.5 years ago by ★ 1.2k
13
votes
8
replies
4.3k
views
Tool: MSigDB for Multiple Organisms in a Tidy Data Format
msigdb pathways R gsea
updated 10 months ago by 43k • written 6.1 years ago by 13k
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 11.5 years ago by 100k
13
votes
1
reply
4.6k
views
Tool: sam2pairwise: a tool to visualize SAM entries as pairwise alignments
sam alignment
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 310
13
votes
7
replies
9.7k
views
Tool: Command-Line Software For Bigwig Data
bigwig
updated 10 months ago by 43k • written 10.5 years ago by ▴ 90
13
votes
14
replies
2.3k
views
Tool: Collaboration on an empirical QC tool
RNA-Seq QC sequencing
updated 10 months ago by 43k • written 7.0 years ago by 54k
13
votes
25
replies
11k
views
9 follow
Tool: Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
analysis sequencing ngs
updated 10 months ago by 43k • written 10.7 years ago by 3.5k
13
votes
0
replies
2.8k
views
Tool: Book: GNU Parallel 2018 - for beginners and advanced users
parallel ngs
updated 10 months ago by 43k • written 5.5 years ago by ★ 4.4k
733 results • Page 2 of 15
Recent Votes
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
A: After read mapping, count exons or genes?
After read mapping, count exons or genes?
Merging a large number of VCF files
A: Merging a large number of VCF files
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
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Popular Question to SHN ▴ 40
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Recent Replies
Comment: filtering before dada2 by GenoMax 142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download by GenoMax 142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified. by GenoMax 142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis by Gordon Smyth ★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
Comment: The GDC Legacy Archive is retiring soon. by lcordeiro ▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome by chrchang523 10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file? by chrchang523 10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
Answer: visualize GSEA by bk11 ★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R by swbarnes2 14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R by Erina • 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read by swbarnes2 14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Mbofire • 0
I need assistance don't know what to do next after signing up
Comment: Easy way to find out which allele is minor allele from bed file? by curious ▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file by GenoMax 142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme by e.r.zakiev ▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
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