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516 results • Page 3 of 11
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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 11 months ago by 43k • written 7.6 years ago by ▴ 80
8
votes
6
replies
3.8k
views
Tool: New ultraperformant version of SICER/epic: epic2
ChIP-Seq
updated 11 months ago by 43k • written 5.5 years ago by ▴ 110
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
27
votes
6
replies
16k
views
Tool: Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
awk
updated 10 months ago by 43k • written 11.9 years ago by 100k
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
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
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
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
2
votes
6
replies
3.4k
views
Tool: microbiomeMarker: microbiome biomarker analysis in R
stamp microbiome lefse
updated 11 months ago by 43k • written 3.9 years ago by ▴ 30
3
votes
5
replies
2.8k
views
Tool: Extend 3' UTR of a GTF file
annotation python RNA-Seq GTF
updated 11 months ago by 43k • written 3.6 years ago by ★ 1.4k
11
votes
5
replies
2.6k
views
Tool: A resource with diverse databases and tools for SARS-CoV-2 (COVID-19) bioinformatics -- Updates
SARS-CoV-2 Corona Databases COVID-19
updated 11 months ago by 43k • written 4.2 years ago by ▴ 270
8
votes
5
replies
4.7k
views
Tool: GFF3 to EMBL converter
gff3 embl
updated 11 months ago by 43k • written 6.7 years ago by 8.6k
2
votes
5
replies
3.8k
views
Tool: Stacks: Pipeline For Building Loci Out Of A Set Of Short-Read Sequenced Samples Of Rad-Seq
Stacks
updated 10 months ago by 43k • written 11.9 years ago by 100k
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
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
8
votes
5
replies
2.9k
views
Tool: Sequence filtration tool
fasta sequence filter
updated 11 months ago by 43k • written 7.2 years ago by ▴ 110
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
2
votes
5
replies
3.2k
views
Tool: Gencove Open and free API. Any DNA data from any type to VCF in 10 to 30 mins.
VCF API imputation
updated 11 months ago by 43k • written 6.6 years ago by ▴ 30
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
2
votes
5
replies
3.2k
views
Tool: tool to reorder mate reads after preprocessing
RNA-Seq
updated 10 months ago by 43k • written 9.7 years ago by ▴ 90
10
votes
5
replies
2.5k
views
Tool: Genozip: A new compression tool for FASTQ, BAM, VCF and more
bam vcf fastq compression
10 months ago by Divon ▴ 230
1
vote
5
replies
2.2k
views
Tool: Open Targets Genetics: variant-centric resource for drug target identification and prioritisation
gene drug GWAS SNP phenotype
updated 11 months ago by 43k • written 5.5 years ago by ★ 5.2k
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
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
4
votes
5
replies
4.4k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 3 days ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
4
votes
5
replies
2.6k
views
Tool: pytfmpval: Efficient, accurate p-value computation for position weight matrices
ChIP-Seq p-value motifs python pwm
updated 11 months ago by 43k • written 5.7 years ago by ★ 16k
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
6
votes
5
replies
13k
views
Tool: Annovar: Functional Annotation Of Genetic Variants From High-Throughput Sequencing Data
annovar
updated 10 months ago by 43k • written 11.9 years ago by 100k
4
votes
4
replies
2.4k
views
Tool: kraken2table, an analogous to kaiju2table
kaiju classification kraken taxonomy
updated 11 months ago by 43k • written 3.8 years ago by ★ 3.6k
9
votes
4
replies
2.3k
views
Tool: SEDA (SEquence DAtaset builder): a desktop tool for processing FASTA files containing DNA and protein sequences
fasta sequences java
5 months ago by Hugo ▴ 380
1
vote
4
replies
3.8k
views
Tool: An easy way to find appropriated tools : OMIC-tools
alignment Assembly sequence genome RNA-Seq
updated 10 months ago by 43k • written 7.9 years ago by ★ 1.4k
1
vote
4
replies
2.5k
views
Tool: Human snoRNA atlas from small RNA sequencing data in deepBase
snoRNA small-RNA-sequencing expression cancer
updated 10 months ago by 43k • written 8.3 years ago by ▴ 860
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
4
replies
2.3k
views
Tool: The Gatk Has A New Website And Forum!
gatk
updated 10 months ago by 43k • written 11.8 years ago by ★ 1.2k
1
vote
4
replies
436
views
Tool: A c library for reading and writing sequences in fasta and fastq format.
seqio
10 weeks ago by dwpeng ▴ 10
5
votes
4
replies
4.2k
views
Tool: Cubemaker - visualize three-dimensional datasets via the web
utility visualization
updated 10 months ago by 43k • written 8.5 years ago by 35k
2
votes
4
replies
1.8k
views
Tool: genomepy: download genomes the easy way
next-gen-sequencing genome alignment ChIP-Seq
updated 11 months ago by 43k • written 6.7 years ago by ▴ 270
4
votes
4
replies
4.3k
views
Tool: Hyphy: Hypothesis Testing Using Phylogenies
phylogeny
updated 10 months ago by 43k • written 11.9 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
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
3
votes
4
replies
1.5k
views
Tool: SIMON says: Powerful, flexible, open-source and easy to use automated machine learning knowledge discovery platform
big-data machine-learning autoML systems-biology
updated 11 months ago by 43k • written 5.1 years ago by ▴ 20
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
9
votes
4
replies
2.7k
views
Tool: Compareads: Comparing Huge Metagenomic Experiments
metagenomics denovo next-gen
updated 10 months ago by 43k • written 11.3 years ago by ▴ 180
5
votes
4
replies
1.6k
views
Tool: pyncls not dead! The datastructure nested containment list (faster than intervaltrees) revived
nested-containment-list python
updated 11 months ago by 43k • written 6.0 years ago by ▴ 960
12
votes
4
replies
1.1k
views
Tool: BBTools 39.03 released!
BBTools BBMap
7 months ago by Brian Bushnell 20k
1
vote
4
replies
2.5k
views
Tool: Multiple Sequence Alignment in the Browser with custom monospace fonts
sequence MSA alignment
updated 11 months ago by 43k • written 5.1 years ago by ★ 1.2k
6
votes
4
replies
1.4k
views
Tool: ctDNAtools: an R package to work with ctDNA sequencing data
cancer-genomics ngs liquid-biopsy sequencing ctdna
updated 11 months ago by 43k • written 4.3 years ago by ▴ 100
7
votes
4
replies
4.6k
views
Tool: RNA Motifs and CLIP-seq database from PAR-CLIP, iCLIP, eCLIP, dCLIP, CLASH, CLEAR-CLIP, irCLIP,sCLIP, hiCLIP and uvCLIP
iCLIP PAR-CLIP HITS-CLIP eCLIP
updated 11 months ago by 43k • written 5.7 years ago by ▴ 860
3
votes
4
replies
1.1k
views
Tool: SRA Run Collector Google Sheets Add-on: Looking for feedback!
RNA-Seq
updated 11 months ago by 43k • written 4.8 years ago by ▴ 30
7
votes
4
replies
2.9k
views
Tool: TreeView3 - An update to java TreeView
TreeView3 java
updated 9 months ago by ▴ 10 • written 5.9 years ago by ▴ 180
516 results • Page 3 of 11
Recent Votes
Answer: Ti Tv ratio and their usefulness in exome sequencing
Answer: Ti Tv ratio and their usefulness in exome sequencing
Answer: How do you generate TMM normalized counts using EdgeR?
Answer: How do you generate TMM normalized counts using EdgeR?
Analysing Microarray Data In Bioconductor
Answer: Q: GenomeScope input and how to interpret the results
Answer: How to find tandem duplications pattern in a DNA sequence
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Recent Replies
Answer: How to find identical sequences in genome fasta file (by Python or any possible by GenoMax 142k
> My final purpose are find and remove any identical sequences present in my genome fasta file. You can use `clumpify.sh` from BBMap suite…
Comment: GO analysis: Indicate genes corresponding to the pathway by marco.barr ▴ 130
I think you have set a filter to get these pahways upstream from the DEG results. You should extract the IDs or names of the genes that you…
Comment: GATK Structural Variants Pipeline - Steps by Bioinformatics_begginner ▴ 20
Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference us…
Comment: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from by GenoMax 142k
Please accept the answer (green check mark) to provide closure to this thread.
Answer: GATK Structural Variants Pipeline - Steps by Pierre Lindenbaum 161k
> A structural variation pipeline for short-read sequencing https://github.com/broadinstitute/gatk-sv
Comment: GATK Structural Variants Pipeline - Steps by DGTool ▴ 20
If it is just the tools that they used which you are looking for, the first link in the overview section of that page leads to the followin…
Comment: GO analysis: p-value range by Matthias Zepper 4.6k
It is just a warning that you add a new scale to a ggplot2 plot, that already has an existing one, which will get replaced. Nothing to worr…
Comment: GO analysis: p-value range by marco.barr ▴ 130
If you write me the code you used I can help you more
Comment: GO analysis: p-value range by sooni ▴ 20
When I run the code, the following message appears: Scale for y is already present. Adding another scale for y, which will replace…
Comment: Why most genes have high padj values by mnx0723 • 0
In the case of other samples, the total number of genes is at least 3,000 more than that one, but it seems to be a relatively small number.…
Comment: How to hide label in layout file of MCscan (python version) by jinyi • 0
Command line is as follows: python -m jcvi.graphics.synteny Cs.Cm.i1.blocks Cs_Cm.bed layout2.txt
Comment: Add stats to the plot by marco.barr ▴ 130
Thank you, it seems to be clearer. Your Condition already has two factorial levels. You can replace these names in groups 1 and 2. da…
Comment: Error in using BioSampleParser tool: subscript out of bounds by marco.barr ▴ 130
Hi, I also had the same problem. If you check its github page there have been no releases for many years and these errors cannot be fixed. …
Comment: Add stats to the plot by Ghada • 0
Thanks, thats really helpful ![enter image description here][1] ![enter image description here][2] [1]: /media/images/0470f3dc-5945-…
Comment: PCA Visualization error in R by marco.barr ▴ 130
SNPRelate is an R package that is able to read from VCF files directly and perform PCA and IBD/IBS. See the documentation for details in Bi…
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