What are the best open-source alternatives to Htseq?

Question 1

Accepted Answer

14 open-source projects similar to htseq/htseq, ranked by shared features. Top picks: alexdobin/star, ayyucedemirbas/scanalyzer, bustools/bustools, combine-lab/alevin-fry, dfajar2/bigscale, diazlab/scell, imb-computational-genomics-lab/ascend, jamesjcai/scgeatoolbox, jhu99/scbean, pachterlab/kallisto.

Question 2

Is alexdobin/star a good alternative to Htseq?

Accepted Answer

RNA-seq aligner

Question 3

Is ayyucedemirbas/scanalyzer a good alternative to Htseq?

Accepted Answer

ayyucedemirbas/scanalyzer is an open-source alternative to Htseq.

Question 4

Is bustools/bustools a good alternative to Htseq?

Accepted Answer

bustools/bustools is an open-source alternative to Htseq.

Question 5

Is combine-lab/alevin-fry a good alternative to Htseq?

Accepted Answer

combine-lab/alevin-fry is an open-source alternative to Htseq.

Question 6

Is dfajar2/bigscale a good alternative to Htseq?

Accepted Answer

dfajar2/bigscale is an open-source alternative to Htseq.

Question 7

Is diazlab/scell a good alternative to Htseq?

Accepted Answer

diazlab/scell is an open-source alternative to Htseq.

Question 8

Is imb-computational-genomics-lab/ascend a good alternative to Htseq?

Accepted Answer

imb-computational-genomics-lab/ascend is an open-source alternative to Htseq.

Question 9

Is jamesjcai/scgeatoolbox a good alternative to Htseq?

Accepted Answer

jamesjcai/scgeatoolbox is an open-source alternative to Htseq.

Question 10

Is jhu99/scbean a good alternative to Htseq?

Accepted Answer

jhu99/scbean is an open-source alternative to Htseq.

Question 11

Is pachterlab/kallisto a good alternative to Htseq?

Accepted Answer

pachterlab/kallisto is an open-source alternative to Htseq.

Open-source alternatives to Htseq

alexdobin/STAR

ayyucedemirbas/scAnalyzer

BUStools/bustools

COMBINE-lab/alevin-fry

dfajar2/bigSCale

diazlab/SCell

IMB-Computational-Genomics-Lab/ascend

jamesjcai/scGEAToolbox

Open-source alternatives to Htseq

alexdobin/STAR

ayyucedemirbas/scAnalyzer

BUStools/bustools

COMBINE-lab/alevin-fry

dfajar2/bigSCale

diazlab/SCell

IMB-Computational-Genomics-Lab/ascend

jamesjcai/scGEAToolbox

jhu99/scbean

pachterlab/kallisto

satijalab/seurat

sdparekh/zUMIs

theislab/scanpy

zhanghao-njmu/SCP