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734 results • Page 3 of 15
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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
2
votes
8
replies
3.7k
views
Tool: Mirnakey - A Software Pipeline For The Analysis Of Microrna Deep Sequencing Data
mirna
updated 10 months ago by 43k • written 11.7 years ago by 100k
2
votes
7
replies
2.9k
views
Tool: An online cute tool to query tumor-gene data from MSK-IMPACT project
MSK-IMPACT tumor mutation MSK
updated 10 months ago by 43k • written 7.0 years ago by ★ 2.5k
4
votes
7
replies
4.6k
views
6 follow
Tool: MAGERI: a software tool for calling rare variants and detecting circulating tumor DNA from UMI-tagged high-throughput sequencing data
rare-variant resequencing umi ctDNA
updated 3 months ago by • 0 • written 7.0 years ago by 3.5k
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
54
votes
7
replies
4.0k
views
6 follow
Tool: Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinformatics
genome-viewer
updated 10 months ago by 43k • written 11.0 years ago by ▴ 40
9
votes
7
replies
3.0k
views
Tool: DiffBind 3.0: Extensive updates in Bioconductor 3.12
DiffBind ChIP-Seq diffbind ATAC-seq chipseq
updated 11 months ago by 43k • written 3.5 years ago by ★ 2.0k
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 8.6 years ago by ▴ 860
3
votes
7
replies
1.4k
views
Tool: New method for protein secondary structure prediction
protein secondary-structure
updated 10 months ago by 43k • written 4.7 years ago by ▴ 180
13
votes
7
replies
9.8k
views
Tool: Command-Line Software For Bigwig Data
bigwig
updated 10 months ago by 43k • written 10.5 years ago by ▴ 90
5
votes
7
replies
3.7k
views
Tool: CircTools: Softwares for Discovering circRNA-microRNA Interactions from CLIP-Seq Datasets
circRNA CLIP-seq microRNA RNA-seq Interactome
updated 10 months ago by 43k • written 6.0 years ago by ▴ 860
6
votes
7
replies
2.5k
views
Tool: Workflow for structural variants from long read sequencing data
structural-variation pacbio nanopore snakemake
updated 10 months ago by 43k • written 5.6 years ago by 47k
4
votes
7
replies
1.4k
views
Tool: Elloreas, a new genome assembler
Assembly next-gen
updated 10 months ago by 43k • written 3.9 years ago by ★ 1.2k
7
votes
7
replies
4.7k
views
Tool: Variant Annotation, Analysis and Search Tool - VAAST2
VAAST2 VAAST
updated 10 months ago by 43k • written 10.0 years ago by 12k
2
votes
7
replies
2.7k
views
Tool: metaflagstat.py - painless bam/sam read flag counting
samtools bam
updated 10 months ago by 43k • written 9.7 years ago by 13k
12
votes
7
replies
3.2k
views
Tool: Chromozoom: The Genome Browser That Lets You Fly!
genome-browser browser
updated 10 months ago by 43k • written 11.2 years ago by 100k
6
votes
7
replies
3.1k
views
Tool: MutScan: detect and visualize target mutations by just scanning FastQ, 50X faster than normal pipelines
Mutation FastQ MutScan OpenGene
updated 10 months ago by 43k • written 7.1 years ago by ★ 2.5k
9
votes
7
replies
3.5k
views
Tool: metaViC: Virus metagenomics pipeline for unknown host or in absence of a host genome
Assembly metagenomics ngs
updated 10 months ago by 43k • written 7.7 years ago by 5.3k
9
votes
7
replies
1.7k
views
Tool: miniDBG - a Jupyter notebook for teaching De Bruijn Graph assembly
python deBruijnGraph de_bruijn_graph assembly teaching
2.0 years ago by Michael 54k
28
votes
7
replies
11k
views
Tool: Quast Is A Convenient Tool For Assembly Evaluation
assembly quality
updated 10 months ago by 43k • written 11.2 years ago by ★ 1.3k
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
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
53
votes
6
replies
9.8k
views
8 follow
Tool: list of dockerized bioinformatics apps
docker
updated 2.3 years ago by 43k • written 9.5 years ago by ★ 3.6k
8
votes
6
replies
3.7k
views
Tool: New ultraperformant version of SICER/epic: epic2
ChIP-Seq
updated 10 months ago by 43k • written 5.5 years ago by ▴ 110
4
votes
6
replies
2.6k
views
Tool: How to find the Genes present in the sequence?
gene genome sequence
updated 22 months ago by 43k • written 9.0 years ago by ▴ 60
5
votes
6
replies
4.5k
views
Tool: Filter VCFs with ExAC data
next-gen SNVs exome filter
updated 2.3 years ago by 43k • written 9.5 years ago by ▴ 40
4
votes
6
replies
5.8k
views
Tool: Fungal genome annotation
genome sequencing
updated 2.4 years ago by 43k • written 9.3 years ago by ▴ 90
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
2
votes
6
replies
3.4k
views
Tool: microbiomeMarker: microbiome biomarker analysis in R
stamp microbiome lefse
updated 10 months ago by 43k • written 3.9 years ago by ▴ 30
4
votes
6
replies
4.4k
views
Tool: StrainControl Laboratory Manager software
LIMS Lab-management Lab-database
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 20
13
votes
6
replies
4.9k
views
Tool: GAWN - Genome Annotation Without Nightmares
genome-annotation
updated 10 months ago by 43k • written 6.8 years ago by 11k
4
votes
6
replies
5.3k
views
Tool: NtSeq: JavaScript bioinformatics library for nucleotide sequence manipulation and analysis.
alignment JavaScript sequence
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 60
6
votes
6
replies
4.8k
views
Tool: Reading/ Writing FASTA files in Java
FASTA Java
updated 10 months ago by 43k • written 9.4 years ago by • 0
12
votes
6
replies
3.5k
views
Tool: Variant annotation and filtration server ALAPY Genome Explorer (AGx)
vcf variant-annotation variant-interpretation
updated 10 months ago by 43k • written 7.0 years ago by ★ 2.8k
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
1
vote
6
replies
2.1k
views
Tool: CSBB [Computational Suite For Biologists and Bioinformaticians]
perl RNA-Seq R
updated 13 months ago by 43k • written 7.9 years ago by • 0
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
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
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
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
0
votes
6
replies
1.5k
views
Tool: Script: Downloading fastq files from ENA database
next-gen-sequencing RNA-Seq
updated 10 months ago by 43k • written 3.3 years ago by • 0
4
votes
6
replies
2.7k
views
Tool: Bamchop: Efficient Digest Of High-Throughput Sequencing Data In A Reproducible Report
bam
updated 10 months ago by 43k • written 10.7 years ago by 22k
2
votes
6
replies
2.1k
views
Tool: Primer design shiny app
SNP sequencing
updated 10 months ago by 43k • written 7.6 years ago by ▴ 10
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 10 months ago by 43k • written 6.3 years ago by 24k
32
votes
6
replies
12k
views
Tool: FASTA and FASTQ tools
Cpp FASTA Python FASTQ
updated 16 months ago by 43k • written 8.9 years ago by ★ 2.3k
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
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
22
votes
5
replies
8.4k
views
Tool: Salmon: A fast and versatile new tool for RNA-seq quantification
RNA-Seq
updated 2.2 years ago by 43k • written 9.4 years ago by 6.5k
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
8
votes
5
replies
2.8k
views
Tool: Sequence filtration tool
fasta sequence filter
updated 10 months ago by 43k • written 7.2 years ago by ▴ 110
734 results • Page 3 of 15
Recent Votes
Answer: How to compute TPM normalized values for TCGA miRNA data?
C: Convert .Txt File To Bed File
A: Get nonoverlapping regions of two bed files
Get nonoverlapping regions of two bed files
Answer: install package
Answer: How I do lift over a Plink bim file from Hg18 to Hg19.
Answer: joint callset and vcf sorting, unknown TAG issue
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Popular Question to rj.rezwan • 0
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Recent Replies
Comment: Extracting mutation status from MAF files - TCGA by Zhenyu Zhang ★ 1.2k
you can assume all genes without mutation is WT (easy) while controlling for (difficult) - coverage - capture region - germline - the …
Comment: Obtaining Infinium Methylation450K manifest for hg38 by Zhenyu Zhang ★ 1.2k
Since you are getting data from the GDC, analysis-related reference/annotations can be found in the GDC reference page here https://gdc.can…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py by fracarb8 ★ 1.6k
I saw that, but considering that your analysis is in seurat and that both liana and liana+ are from the same developers, it might be quicke…
Answer: Nomalization - TCGA, RNA-seq and Microarray by Zhenyu Zhang ★ 1.2k
You can rank normalize them, but to tell the truth, I won't trust any conclusion you can draw from such combined data. The recommended …
Comment: How to remove multiple batch effects from RNA-seq data before limma differential by ATpoint 82k
Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
Comment: Longest transcript variant per gene by sansan_96 ▴ 90
Thank you very much, success in your projects.
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Thanks for the input :)
Comment: install package: package ‘gmwm’ is not available for this version of R by Pine ▴ 20
This seems to indicate that the package itself (or packages it depends on) are not compatible with the R version you are using. Next step c…
Answer: Tissue-specific DEG analysis with DEseq2 by arctic ▴ 40
Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by Pierre Lindenbaum 161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by ajbarrett98 • 0
Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
Answer: Practical Haplotype Graph v2 not finding correct paths by pjb39 ▴ 200
There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
Comment: Output file of satools flagstat empty by Mathew ▴ 100
Hi, In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…
Comment: Tissue-specific DEG analysis with DEseq2 by BioinfGuru ★ 1.7k
I wrote an R package (see [rrdr.io][1], and [github][2]) some years ago to calculate tissue specificity from bulk RNAseq based on [this pap…
Comment: joint callset and vcf sorting, unknown TAG issue by Pierre Lindenbaum 161k
> set the Number= to 0 instead of 1; I'm not sure it's a problem. > probably I should also change the Type to Flag ah yes, my bad ! (f…
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