A method for determining the numbers of targets, comprising: (a) stochastically barcoding a plurality of targets of a sample comprising one or more cells, wherein the targets comprise target nucleic acids, using a plurality of stochastic barcodes to create a plurality of stochastically barcoded targets, wherein each of the stochastic barcodes is a nucleic acid barcode, wherein each of the plurality of stochastic barcodes comprises a molecular label; (b) obtaining sequencing data of the stochastically barcoded targets; and (c) for one or more of the plurality of targets: (i) counting the number of molecular labels with distinct sequences associated with the target in the sequencing data; (ii) identifying clusters of molecular labels of the target using directional adjacency; (iii) collapsing the sequencing data obtained in (b) using the clusters of molecular labels of the target identified in (ii); and (iv) estimating the number of the target, wherein the number of the target estimated correlates with the number of molecular labels with distinct sequences associated with the target in the sequencing data counted in (i) after collapsing the sequencing data in (ii), comprising: fitting the distribution of the molecular labels of the target and their occurrences to two negative binomial distributions; determining the number of true molecular labels n using the two negative binomial distributions; and removing the false molecular labels from the sequencing data obtained in (b), wherein the false molecular labels comprise molecular labels with occurrences lower than the occurrence of the nth most abundant molecular label, and wherein the true molecular labels comprise molecular labels with occurrences greater than or equal to the occurrence of the nth most abundant molecular label. (a) stochastically barcoding a plurality of targets of a sample comprising one or more cells, wherein the targets comprise target nucleic acids, using a plurality of stochastic barcodes to create a plurality of stochastically barcoded targets, wherein each of the stochastic barcodes is a nucleic acid barcode, wherein each of the plurality of stochastic barcodes comprises a molecular label; (b) obtaining sequencing data of the stochastically barcoded targets; and (c) for one or more of the plurality of targets: (i) counting the number of molecular labels with distinct sequences associated with the target in the sequencing data; (ii) identifying clusters of molecular labels of the target using directional adjacency; (iii) collapsing the sequencing data obtained in (b) using the clusters of molecular labels of the target identified in (ii); and (iv) estimating the number of the target, wherein the number of the target estimated correlates with the number of molecular labels with distinct sequences associated with the target in the sequencing data counted in (i) after collapsing the sequencing data in (ii), comprising: fitting the distribution of the molecular labels of the target and their occurrences to two negative binomial distributions; determining the number of true molecular labels n using the two negative binomial distributions; and removing the false molecular labels from the sequencing data obtained in (b), wherein the false molecular labels comprise molecular labels with occurrences lower than the occurrence of the nth most abundant molecular label, and wherein the true molecular labels comprise molecular labels with occurrences greater than or equal to the occurrence of the nth most abundant molecular label. (i) counting the number of molecular labels with distinct sequences associated with the target in the sequencing data; (ii) identifying clusters of molecular labels of the target using directional adjacency; (iii) collapsing the sequencing data obtained in (b) using the clusters of molecular labels of the target identified in (ii); and (iv) estimating the number of the target, wherein the number of the target estimated correlates with the number of molecular labels with distinct sequences associated with the target in the sequencing data counted in (i) after collapsing the sequencing data in (ii), comprising: fitting the distribution of the molecular labels of the target and their occurrences to two negative binomial distributions; determining the number of true molecular labels n using the two negative binomial distributions; and removing the false molecular labels from the sequencing data obtained in (b), wherein the false molecular labels comprise molecular labels with occurrences lower than the occurrence of the nth most abundant molecular label, and wherein the true molecular labels comprise molecular labels with occurrences greater than or equal to the occurrence of the nth most abundant molecular label. fitting the distribution of the molecular labels of the target and their occurrences to two negative binomial distributions; determining the number of true molecular labels n using the two negative binomial distributions; and removing the false molecular labels from the sequencing data obtained in (b), wherein the false molecular labels comprise molecular labels with occurrences lower than the occurrence of the nth most abundant molecular label, and wherein the true molecular labels comprise molecular labels with occurrences greater than or equal to the occurrence of the nth most abundant molecular label.