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733 results • Page 2 of 15
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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
83
votes
46
replies
8.9k
views
15 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
updated 6 weeks ago by 4.2k • written 10 months ago by ▴ 840
6
votes
3
replies
8.8k
views
Tool: Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analysis
chip-seq
updated 10 months ago by 43k • written 11.2 years ago by 6.0k
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
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
9
votes
1
reply
8.6k
views
Tool: Rseqqc And Rna-Seqqc - Quality Control Software For Rna-Seq Data
rna-seq qc
updated 10 months ago by 43k • written 11.7 years ago by 100k
22
votes
4
replies
8.6k
views
Tool: Very Bad Things
python text
updated 16 months ago by 43k • written 11.2 years ago by 24k
22
votes
5
replies
8.4k
views
Tool: Salmon: A fast and versatile new tool for RNA-seq quantification
RNA-Seq
updated 2.1 years ago by 43k • written 9.4 years ago by 6.5k
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
48
votes
24
replies
8.2k
views
14 follow
Tool: Hera: A new tool for RNA-Seq analysis
kallisto RNA-Seq STAR gene-fusion
updated 10 months ago by 43k • written 6.8 years ago by ▴ 580
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 6.1 years ago by ★ 1.3k
4
votes
0
replies
8.1k
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 9.9 years ago by ▴ 670
3
votes
1
reply
7.9k
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
7.8k
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
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 7.7 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
7.6k
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
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 9.5 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 11.5 years ago by 24k
0
votes
2
replies
7.5k
views
Tool: The script to install the required packages for gene expression analysis using DESeq2 for downstream analysis and visualization
R RNAseq installation DESeq2
8 months ago by Aditya naman • 0
10
votes
2
replies
7.4k
views
Tool: fastp, the ultra-fast FASTQ preprocessing tool, is now on BioConda
fastp
updated 13 months ago by 43k • written 6.3 years ago by ★ 2.5k
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
4
votes
3
replies
7.2k
views
Tool: Deindexer - A Standalone Demultiplexing Tool For Illumina Platform
illumina
updated 10 months ago by 43k • written 11.3 years ago by ▴ 110
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
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
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 12 months ago by 43k • written 7.6 years ago by ▴ 860
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 6.3 years ago by ▴ 60
11
votes
2
replies
7.0k
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 5.8 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
4
votes
2
replies
6.6k
views
Tool: pdb-tools: a set of Python scripts to manipulate PDB files.
python pdb modeling
updated 22 months ago by 43k • written 9.0 years ago by ★ 2.5k
22
votes
8
replies
6.5k
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
1
vote
0
replies
6.5k
views
Tool: Free available Supercomputing services - List
Supercomputing grid Assembly annotation
updated 22 months ago by 43k • written 9.0 years ago by ▴ 50
11
votes
14
replies
6.4k
views
6 follow
Tool: [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
python genbank sequence cds protein
updated 2.2 years ago by 43k • written 9.5 years ago by ▴ 130
7
votes
6
replies
6.4k
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 7.5 years ago by ▴ 80
3
votes
8
replies
6.2k
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
6.2k
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
11
votes
7
replies
6.2k
views
Tool: RNA Modification Database and Epitranscriptome Sequencing Data
Epitranscriptome m5C m6A RNA-modification m1A
updated 20 months ago by 43k • written 8.5 years ago by ▴ 860
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
2
votes
5
replies
6.1k
views
Tool: umitools - working with UMI incorporated data
UMI sequencing
updated 10 months ago by 43k • written 9.8 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
12
votes
5
replies
6.1k
views
Tool: AGAT - Another Gff/Gtf Analysis Toolkit
gff gtf
updated 10 months ago by 43k • written 4.4 years ago by 8.5k
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
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
733 results • Page 2 of 15
Recent Votes
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: NGS forensics: how to know if data is fabricated by i.sudbery 19k
I don't follow your argument for distinguishing between genomic contamination and freud. A data set being bad in terms of genomic contamin…
Comment: What does it mean single base resolution in sequencing? by jinyu ▴ 10
Thank you for your detail and great explanation. I do need more time to understand these. And there is still something compuzzling me. For …
Answer: Is it possible to bulk download files from GEO repository? by atharvakarkare14 ▴ 10
Try using this library [GEOparse][1] [1]: https://github.com/guma44/GEOparse
Answer: How many reads for WGS Sequencing? by Ruqaiya • 0
OK. Problem solved. The problem was from my end. Thank you both for helping !!
Comment: NGS forensics: how to know if data is fabricated by Mensur Dlakic ★ 27k
Appreciate the suggestion, but that ship has sailed and reached the other shore. This happened 10+ years ago. To the best of my knowledge n…
Comment: Figures are disappeared from html report of SnpEff by analyst ▴ 30
Files are not opening in any of the computer (ubuntu/windows). I rereun snpEff annotation but still output html files are having missing im…
Comment: Figures are disappeared from html report of SnpEff by analyst ▴ 30
I reinstalled nodejs: > sudo apt-get install nodejs Its already up to date with version v10.19.0
Answer: NGS forensics: how to know if data is fabricated by Prash ▴ 280
Mensur, if I were you, I'd probably contact the CA directly and check with him whether they have reproduced the works recently. There coul…
Comment: NGS forensics: how to know if data is fabricated by noodle ▴ 560
Working on it - it's actually a bit difficult. Low coverage of ribosomal proteins. Low coverage of housekeeping genes ...I'm trying to find…
Comment: NGS forensics: how to know if data is fabricated by noodle ▴ 560
I'm a bit against pubpeer - have you ever posted there? My gripe with them is that the posts are heavily moderated and EDITED to the point…
Comment: NGS forensics: how to know if data is fabricated by Philipp Bayer 8.4k
Thanks Mensur! I'd add that in 9 out of 10 cases, you won't receive a reply to a request for raw data. That's just how scientists are, does…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
I had downloaded the two files in a similar manner actually.
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
ok, i'll try to use fastp. I have only used trimmomatic and cutadapt till now and they dont identify on its own. Except the graph in fastqc…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
got it! even if i'm doing the assembly for paired end with both the files do i have set the threshold to 1000bp ?
Comment: NGS forensics: how to know if data is fabricated by Philipp Bayer 8.4k
i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
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