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736 results • Page 3 of 15
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3
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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 12.0 years ago by ▴ 170
12
votes
8
replies
3.2k
views
Tool: BioBit: Global bioinformatics chat
communication
updated 13 months ago by 43k • written 7.9 years ago by ▴ 90
7
votes
7
replies
4.7k
views
Tool: Variant Annotation, Analysis and Search Tool - VAAST2
VAAST2 VAAST
updated 10 months ago by 43k • written 10.1 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
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
3.6k
views
Tool: metaViC: Virus metagenomics pipeline for unknown host or in absence of a host genome
Assembly metagenomics ngs
updated 11 months ago by 43k • written 7.7 years ago by 5.3k
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
3
votes
7
replies
1.4k
views
Tool: New method for protein secondary structure prediction
protein secondary-structure
updated 11 months ago by 43k • written 4.7 years ago by ▴ 180
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
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 3.6 years ago by ★ 2.0k
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
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
13
votes
7
replies
9.8k
views
Tool: Command-Line Software For Bigwig Data
bigwig
updated 11 months ago by 43k • written 10.5 years ago by ▴ 90
4
votes
7
replies
1.4k
views
Tool: Elloreas, a new genome assembler
Assembly next-gen
updated 11 months ago by 43k • written 3.9 years ago by ★ 1.2k
6
votes
7
replies
2.5k
views
Tool: Workflow for structural variants from long read sequencing data
structural-variation pacbio nanopore snakemake
updated 11 months ago by 43k • written 5.6 years ago by 47k
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
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 11 months ago by 43k • written 6.0 years ago by ▴ 860
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
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
2.1 years ago by Michael 54k
13
votes
7
replies
4.2k
views
Tool: I-PV: a CIRCOS module for interactive protein sequence visualization
interactive javascript circos sequence
updated 21 months ago by 43k • written 8.6 years ago by ★ 1.2k
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
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
18
votes
6
replies
4.9k
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
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
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
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
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
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
0
votes
6
replies
1.5k
views
Tool: Script: Downloading fastq files from ENA database
next-gen-sequencing RNA-Seq
updated 11 months ago by 43k • written 3.3 years ago by • 0
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
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 9.1 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
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
5.2k
views
Tool: Variantannotation Package (Bioconductor)
snp variant-annotation
updated 10 months ago by 43k • written 11.8 years ago by 20k
53
votes
6
replies
9.8k
views
8 follow
Tool: list of dockerized bioinformatics apps
docker
updated 2.3 years ago by 43k • written 9.6 years ago by ★ 3.6k
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
13
votes
6
replies
4.9k
views
Tool: GAWN - Genome Annotation Without Nightmares
genome-annotation
updated 11 months ago by 43k • written 6.8 years ago by 11k
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
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
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
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
5
votes
6
replies
4.6k
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
32
votes
6
replies
12k
views
Tool: FASTA and FASTQ tools
Cpp FASTA Python FASTQ
updated 16 months ago by 43k • written 9.0 years ago by ★ 2.3k
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
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
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
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 6.6k
5
votes
5
replies
2.7k
views
Tool: Building a new NGS analysis platform, we would love your feedback (RNA-seq)
RNA-Seq
updated 21 months ago by 43k • written 8.4 years ago by ▴ 50
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
19
votes
5
replies
8.9k
views
Tool: Automatic IGV snapshot script
ChIP-Seq IGV
updated 14 months ago by 43k • written 7.2 years ago by ★ 3.5k
736 results • Page 3 of 15
Recent Votes
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Recent Replies
Answer: CellRanger output more cells than specified using --force-cells? Why? by scideas ▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data by Muhammad • 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors) by nguyenn6 • 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed by anton.i.petrov • 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
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